Genetic Variant SLC14A1:c.663+669T>C (chr18-45737317-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015865.7(SLC14A1):c.663+669T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 153,098 control chromosomes in the GnomAD database, including 29,102 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.61 ( 28950 hom., cov: 33)

Exomes 𝑓: 0.57 ( 152 hom. )

Consequence

SLC14A1
NM_015865.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0730

Publications

23 publications found

Variant links:

Genes affected

SLC14A1 (HGNC:10918): (solute carrier family 14 member 1 (Kidd blood group)) The protein encoded by this gene is a membrane transporter that mediates urea transport in erythrocytes. This gene forms the basis for the Kidd blood group system. [provided by RefSeq, Mar 2009]

SLC14A1 Gene-Disease associations (from GenCC):

blood group, kidd system
Inheritance: AD Classification: LIMITED Submitted by: PanelApp Australia

SLC14A1 links:

ENSG00000288545 (HGNC:):

ENSG00000288545 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.906 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015865.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC14A1	NM_015865.7	MANE Select	c.663+669T>C	intron	N/A	NP_056949.4	Q13336-1
SLC14A1	NM_001128588.4		c.831+669T>C	intron	N/A	NP_001122060.3	Q13336-2
SLC14A1	NM_001146037.1		c.831+669T>C	intron	N/A	NP_001139509.1	Q13336-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC14A1	ENST00000321925.9	TSL:1 MANE Select	c.663+669T>C	intron	N/A	ENSP00000318546.4	Q13336-1
SLC14A1	ENST00000586142.5	TSL:1	c.663+669T>C	intron	N/A	ENSP00000470476.1	Q13336-1
SLC14A1	ENST00000589700.5	TSL:1	c.663+669T>C	intron	N/A	ENSP00000465044.1	E9NSU1

Frequencies

GnomAD3 genomes

AF:

0.611

AC:

92860

AN:

152034

Hom.:

28923

Cov.:

show subpopulations

Gnomad AFR

AF:

0.649

Gnomad AMI

AF:

0.398

Gnomad AMR

AF:

0.687

Gnomad ASJ

AF:

0.520

Gnomad EAS

AF:

0.928

Gnomad SAS

AF:

0.679

Gnomad FIN

AF:

0.593

Gnomad MID

AF:

0.547

Gnomad NFE

AF:

0.553

Gnomad OTH

AF:

0.595

GnomAD4 exome

AF:

0.571

AC:

540

AN:

946

Hom.:

152

AF XY:

0.552

AC XY:

267

AN XY:

484

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.667

AC:

116

AN:

174

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.875

AC:

AN:

South Asian (SAS)

AF:

0.700

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.538

AC:

367

AN:

682

Other (OTH)

AF:

0.467

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.493

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:

0.611

AC:

92936

AN:

152152

Hom.:

28950

Cov.:

AF XY:

0.614

AC XY:

45684

AN XY:

74394

show subpopulations

African (AFR)

AF:

0.648

AC:

26892

AN:

41468

American (AMR)

AF:

0.688

AC:

10522

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.520

AC:

1801

AN:

3466

East Asian (EAS)

AF:

0.928

AC:

4816

AN:

5190

South Asian (SAS)

AF:

0.678

AC:

3263

AN:

4812

European-Finnish (FIN)

AF:

0.593

AC:

6283

AN:

10594

Middle Eastern (MID)

AF:

0.558

AC:

164

AN:

294

European-Non Finnish (NFE)

AF:

0.553

AC:

37583

AN:

68008

Other (OTH)

AF:

0.593

AC:

1250

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1894

3788

5681

7575

9469

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

772

1544

2316

3088

3860

<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:

0.578

Hom.:

43774

Bravo

AF:

0.619

Asia WGS

AF:

0.770

AC:

2680

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

5.7

(source)

DANN

Benign

0.46

PhyloP100

0.073

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

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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