7-138668442-A-G

Variant names:

• chr7-138668442-A-G
• rs1015343
• NM_001139456.2:c.273+3577T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001139456.2(SVOPL):​c.273+3577T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 151,886 control chromosomes in the GnomAD database, including 19,810 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 0.50 (19810 hom., cov: 31)
• Consequence: SVOPL NM_001139456.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 2 publications found

Genes affected

SVOPL (HGNC:27034): (SVOP like) The protein encoded by this gene is thought to be a member of solute carrier family 22, which includes transmembrane proteins that transport toxins and drugs from the body. This gene is a paralog of the SVOP gene that encodes synaptic vesicle 2-related protein. [provided by RefSeq, Sep 2016]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SVOPL	NM_001139456.2	c.273+3577T>C		intron_variant	Intron 4 of 15	ENST00000674285.1	NP_001132928.1
SVOPL	XM_011515797.3	c.-59+3577T>C		intron_variant	Intron 1 of 11		XP_011514099.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SVOPL	ENST00000674285.1	c.273+3577T>C		intron_variant	Intron 4 of 15		NM_001139456.2	ENSP00000501457.1
SVOPL	ENST00000419765.4	c.273+3577T>C		intron_variant	Intron 3 of 14	5		ENSP00000405482.2
SVOPL	ENST00000421622.5	c.174+9992T>C		intron_variant	Intron 3 of 11	5		ENSP00000412830.1

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76107 AN: 151768 Hom.: 19765 Cov.: 31

Gnomad AFR AF: 0.635

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.514

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.502 AC: 76212 AN: 151886 Hom.: 19810 Cov.: 31 AF XY: 0.498 AC XY: 36944 AN XY: 74220

African (AFR) AF: 0.635 AC: 26316 AN: 41428

American (AMR) AF: 0.461 AC: 7033 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.588 AC: 2038 AN: 3464

East Asian (EAS) AF: 0.564 AC: 2904 AN: 5146

South Asian (SAS) AF: 0.491 AC: 2358 AN: 4800

European-Finnish (FIN) AF: 0.368 AC: 3874 AN: 10538

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.444 AC: 30157 AN: 67926

Other (OTH) AF: 0.516 AC: 1090 AN: 2112

Alfa AF: 0.470 Hom.: 10240

Bravo AF: 0.518

Asia WGS AF: 0.544 AC: 1892 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.38
DANN	Benign	0.16
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1015343; hg19: chr7-138353187;