chr8-100646940-A-G

Variant names:

• chr8-100646940-A-G
• rs7815950
• NM_152628.4:c.141+2334T>C

Variant summary

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

The NM_152628.4(SNX31):​c.141+2334T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0656 in 152,312 control chromosomes in the GnomAD database, including 454 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 0.066 (454 hom., cov: 32)
• Consequence: SNX31 NM_152628.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.374
• Publications: 5 publications found

Genes affected

SNX31 (HGNC:28605): (sorting nexin 31) Predicted to enable phosphatidylinositol binding activity. Predicted to be involved in intracellular protein transport. Predicted to be located in cytoskeleton. Predicted to be part of protein-containing complex. Predicted to be active in early endosome. [provided by Alliance of Genome Resources, Apr 2022]

SNX31 Gene-Disease associations (from GenCC):

• schizophrenia

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0927 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNX31	NM_152628.4	c.141+2334T>C		intron_variant	Intron 2 of 13	ENST00000311812.7	NP_689841.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNX31	ENST00000311812.7	c.141+2334T>C		intron_variant	Intron 2 of 13	2	NM_152628.4	ENSP00000312368.2
SNX31	ENST00000520661.5	c.144+10784T>C		intron_variant	Intron 2 of 4	3		ENSP00000428855.1
SNX31	ENST00000520352.5	c.-57-10929T>C		intron_variant	Intron 1 of 5	3		ENSP00000428210.1
SNX31	ENST00000520743.1	c.219+2334T>C		intron_variant	Intron 3 of 3	4		ENSP00000428262.1

Frequencies

GnomAD3 genomes AF: 0.0656 AC: 9990 AN: 152194 Hom.: 455 Cov.: 32

Gnomad AFR AF: 0.0209

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.0510

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.0277

Gnomad SAS AF: 0.0623

Gnomad FIN AF: 0.0667

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0947

Gnomad OTH AF: 0.0684

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

GnomAD4 genome AF: 0.0656 AC: 9997 AN: 152312 Hom.: 454 Cov.: 32 AF XY: 0.0648 AC XY: 4823 AN XY: 74472

African (AFR) AF: 0.0210 AC: 872 AN: 41586

American (AMR) AF: 0.0510 AC: 780 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 468 AN: 3466

East Asian (EAS) AF: 0.0279 AC: 145 AN: 5190

South Asian (SAS) AF: 0.0628 AC: 303 AN: 4826

European-Finnish (FIN) AF: 0.0667 AC: 707 AN: 10604

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0947 AC: 6439 AN: 68018

Other (OTH) AF: 0.0686 AC: 145 AN: 2114

Alfa AF: 0.0889 Hom.: 378

Bravo AF: 0.0631

Asia WGS AF: 0.0400 AC: 139 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.3
DANN	Benign	0.56
PhyloP100		-0.37
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: rs7815950; hg19: chr8-101659168;