chr7-138598335-T-C

Position:

• chr7-138598335-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001139456.2(SVOPL):​c.1354-1805A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.767 in 152,088 control chromosomes in the GnomAD database, including 46,002 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 0.77 (46002 hom., cov: 31)
• Consequence: SVOPL NM_001139456.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.934 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SVOPL	NM_001139456.2	c.1354-1805A>G		intron_variant		ENST00000674285.1	NP_001132928.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SVOPL	ENST00000674285.1	c.1354-1805A>G		intron_variant			NM_001139456.2	ENSP00000501457	P1

Frequencies

GnomAD3 genomes AF: 0.767 AC: 116498 AN: 151970 Hom.: 45953 Cov.: 31

Gnomad AFR AF: 0.942

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.782

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.736

Gnomad OTH AF: 0.758

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

GnomAD4 genome AF: 0.767 AC: 116590 AN: 152088 Hom.: 46002 Cov.: 31 AF XY: 0.756 AC XY: 56208 AN XY: 74334

Gnomad4 AFR AF: 0.942

Gnomad4 AMR AF: 0.642

Gnomad4 ASJ AF: 0.782

Gnomad4 EAS AF: 0.388

Gnomad4 SAS AF: 0.713

Gnomad4 FIN AF: 0.662

Gnomad4 NFE AF: 0.736

Gnomad4 OTH AF: 0.755

Alfa AF: 0.752 Hom.: 5114

Bravo AF: 0.770

Asia WGS AF: 0.561 AC: 1958 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.0
DANN	Benign	0.79

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

LitVar

Other links and lift over

dbSNP: rs1371463; hg19: chr7-138283080;