Genetic Variant SLC16A1:c.362-34_362-11delTATTTATTTATTTATTTATTTATT (chr1-112918054-CAATAAATAAATAAATAAATAAATA-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The NM_003051.4(SLC16A1):c.362-34_362-11delTATTTATTTATTTATTTATTTATT variant causes a intron change. The variant allele was found at a frequency of 0.000533 in 859,840 control chromosomes in the GnomAD database, including 24 homozygotes. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0017 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00030 ( 24 hom. )

Consequence

SLC16A1
NM_003051.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.97

Publications

1 publications found

Variant links:

Genes affected

SLC16A1 (HGNC:10922): (solute carrier family 16 member 1) The protein encoded by this gene is a proton-linked monocarboxylate transporter that catalyzes the movement of many monocarboxylates, such as lactate and pyruvate, across the plasma membrane. Mutations in this gene are associated with erythrocyte lactate transporter defect. Alternatively spliced transcript variants have been found for this gene.[provided by RefSeq, Oct 2009]

SLC16A1 links:

SLC16A1-AS1 (HGNC:49445): (SLC16A1 antisense RNA 1)

SLC16A1-AS1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6

Variant 1-112918054-CAATAAATAAATAAATAAATAAATA-C is Benign according to our data. Variant chr1-112918054-CAATAAATAAATAAATAAATAAATA-C is described in ClinVar as Benign. ClinVar VariationId is 1672528.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00169 (245/144640) while in subpopulation AFR AF = 0.00588 (228/38748). AF 95% confidence interval is 0.00526. There are 0 homozygotes in GnomAd4. There are 103 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.

BS2

High Homozygotes in GnomAdExome4 at 24 AD,AR,Unknown,SD gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003051.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC16A1	NM_003051.4	MANE Select	c.362-34_362-11delTATTTATTTATTTATTTATTTATT		intron	N/A	NP_003042.3
	SLC16A1	NM_001166496.2		c.362-34_362-11delTATTTATTTATTTATTTATTTATT		intron	N/A	NP_001159968.1	P53985-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC16A1	ENST00000369626.8	TSL:1 MANE Select	c.362-34_362-11delTATTTATTTATTTATTTATTTATT	intron	N/A	ENSP00000358640.4	P53985-1
SLC16A1	ENST00000429288.2	TSL:3	c.362-34_362-11delTATTTATTTATTTATTTATTTATT	intron	N/A	ENSP00000397106.2	P53985-1
SLC16A1	ENST00000443580.6	TSL:3	c.362-34_362-11delTATTTATTTATTTATTTATTTATT	intron	N/A	ENSP00000399104.2	P53985-1

Frequencies

GnomAD3 genomes

AF:

0.00169

AC:

245

AN:

144568

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00590

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000758

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000753

Gnomad OTH

AF:

0.000506

GnomAD4 exome

AF:

0.000298

AC:

213

AN:

715200

Hom.:

AF XY:

0.000262

AC XY:

AN XY:

362046

show subpopulations

African (AFR)

AF:

0.00996

AC:

146

AN:

14652

American (AMR)

AF:

0.000695

AC:

AN:

12942

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

14304

East Asian (EAS)

AF:

0.00

AC:

AN:

24300

South Asian (SAS)

AF:

0.00

AC:

AN:

22964

European-Finnish (FIN)

AF:

0.0000477

AC:

AN:

20954

Middle Eastern (MID)

AF:

0.00136

AC:

AN:

2214

European-Non Finnish (NFE)

AF:

0.0000559

AC:

AN:

572112

Other (OTH)

AF:

0.000715

AC:

AN:

30758

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.704

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00169

AC:

245

AN:

144640

Hom.:

Cov.:

AF XY:

0.00147

AC XY:

103

AN XY:

70222

show subpopulations

African (AFR)

AF:

0.00588

AC:

228

AN:

38748

American (AMR)

AF:

0.000757

AC:

AN:

14538

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3438

East Asian (EAS)

AF:

0.00

AC:

AN:

4984

South Asian (SAS)

AF:

0.00

AC:

AN:

4518

European-Finnish (FIN)

AF:

0.00

AC:

AN:

8802

Middle Eastern (MID)

AF:

0.00

AC:

AN:

284

European-Non Finnish (NFE)

AF:

0.0000753

AC:

AN:

66424

Other (OTH)

AF:

0.000500

AC:

AN:

2000

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.572

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

967

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

4.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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1-112918054-CAATAAATAAATAAATAAATAAATAAATAAATA-CAATAAATA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over