chr7-138598335-T-C

Variant names:

• chr7-138598335-T-C
• rs1371463
• NM_001139456.2:c.1354-1805A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.934 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001139456.2. 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
	SVOPL	NM_001139456.2	MANE Select	c.1354-1805A>G		intron	N/A	NP_001132928.1	Q8N434-1
	SVOPL	NM_001331192.1		c.1081-1805A>G		intron	N/A	NP_001318121.1
	SVOPL	NM_174959.3		c.898-1805A>G		intron	N/A	NP_777619.1	Q8N434-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SVOPL	ENST00000674285.1	MANE Select	c.1354-1805A>G		intron	N/A	ENSP00000501457.1	Q8N434-1
	SVOPL	ENST00000436657.5	TSL:1	c.898-1805A>G		intron	N/A	ENSP00000417018.1	Q8N434-2
	SVOPL	ENST00000419765.4	TSL:5	c.1354-1805A>G		intron	N/A	ENSP00000405482.2	Q8N434-1

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

African (AFR) AF: 0.942 AC: 39128 AN: 41530

American (AMR) AF: 0.642 AC: 9799 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.782 AC: 2713 AN: 3468

East Asian (EAS) AF: 0.388 AC: 2006 AN: 5170

South Asian (SAS) AF: 0.713 AC: 3428 AN: 4806

European-Finnish (FIN) AF: 0.662 AC: 7003 AN: 10574

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.736 AC: 49994 AN: 67952

Other (OTH) AF: 0.755 AC: 1594 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.0
DANN	Benign	0.79
PhyloP100		-1.3
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: rs1371463; hg19: chr7-138283080;