Genetic Variant NM_006671.6:c.216-1025T>C (chr1-53115998-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_006671.6(SLC1A7):c.216-1025T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 152,108 control chromosomes in the GnomAD database, including 23,521 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 0.53 ( 23520 hom., cov: 33)

Exomes 𝑓: 0.50 ( 1 hom. )

Consequence

SLC1A7
NM_006671.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.692

Publications

12 publications found

Variant links:

Genes affected

SLC1A7 (HGNC:10945): (solute carrier family 1 member 7) Predicted to enable anion transmembrane transporter activity. Involved in neurotransmitter reuptake. Predicted to be located in plasma membrane. Predicted to be active in glutamatergic synapse. Predicted to be integral component of postsynaptic membrane and integral component of presynaptic membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLC1A7 links:

ENSG00000235563 (HGNC:):

ENSG00000235563 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=-0.54).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006671.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SLC1A7	NM_006671.6	MANE Select	c.216-1025T>C	intron	N/A	NP_006662.3
SLC1A7	NM_001287595.2		c.216-1025T>C	intron	N/A	NP_001274524.1
SLC1A7	NM_001287597.2		c.216-10224T>C	intron	N/A	NP_001274526.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SLC1A7	ENST00000371494.9	TSL:1 MANE Select	c.216-1025T>C	intron	N/A	ENSP00000360549.5
SLC1A7	ENST00000620347.5	TSL:1	c.216-1025T>C	intron	N/A	ENSP00000478639.1
SLC1A7	ENST00000611397.5	TSL:1	c.216-10224T>C	intron	N/A	ENSP00000484987.1

Frequencies

GnomAD3 genomes

AF:

0.526

AC:

80018

AN:

151982

Hom.:

23488

Cov.:

show subpopulations

Gnomad AFR

AF:

0.748

Gnomad AMI

AF:

0.377

Gnomad AMR

AF:

0.583

Gnomad ASJ

AF:

0.334

Gnomad EAS

AF:

0.877

Gnomad SAS

AF:

0.617

Gnomad FIN

AF:

0.415

Gnomad MID

AF:

0.415

Gnomad NFE

AF:

0.376

Gnomad OTH

AF:

0.499

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

Cov.:

AF XY:

0.750

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.550

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome 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

GnomAD4 genome

AF:

0.527

AC:

80099

AN:

152100

Hom.:

23520

Cov.:

AF XY:

0.532

AC XY:

39551

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.748

AC:

31027

AN:

41490

American (AMR)

AF:

0.584

AC:

8930

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.334

AC:

1158

AN:

3466

East Asian (EAS)

AF:

0.877

AC:

4530

AN:

5168

South Asian (SAS)

AF:

0.618

AC:

2979

AN:

4824

European-Finnish (FIN)

AF:

0.415

AC:

4390

AN:

10576

Middle Eastern (MID)

AF:

0.401

AC:

118

AN:

294

European-Non Finnish (NFE)

AF:

0.376

AC:

25557

AN:

67962

Other (OTH)

AF:

0.504

AC:

1067

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1709

3419

5128

6838

8547

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

678

1356

2034

2712

3390

<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:

0.429

Hom.:

32239

Bravo

AF:

0.548

Asia WGS

AF:

0.755

AC:

2623

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

(source)

DANN

Benign

0.83

PhyloP100

0.69

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