chr8-100646940-A-G

Position:

• chr8-100646940-A-G

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
SNX31	NM_152628.4	c.141+2334T>C		intron_variant		ENST00000311812.7	NP_689841.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNX31	ENST00000311812.7	c.141+2334T>C		intron_variant		2	NM_152628.4	ENSP00000312368	P1
SNX31	ENST00000520352.5	c.-57-10929T>C		intron_variant		3		ENSP00000428210
SNX31	ENST00000520661.5	c.144+10784T>C		intron_variant		3		ENSP00000428855
SNX31	ENST00000520743.1	c.219+2334T>C		intron_variant		4		ENSP00000428262

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

Gnomad4 AFR AF: 0.0210

Gnomad4 AMR AF: 0.0510

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.0279

Gnomad4 SAS AF: 0.0628

Gnomad4 FIN AF: 0.0667

Gnomad4 NFE AF: 0.0947

Gnomad4 OTH AF: 0.0686

Alfa AF: 0.0891 Hom.: 344

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

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: rs7815950; hg19: chr8-101659168;