7-17879635-G-T

Variant names:

• chr7-17879635-G-T
• rs4142995
• ENST00000409604.1:c.*3179C>A

Variant summary

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

The ENST00000409604.1(SNX13):​c.*3179C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 151,998 control chromosomes in the GnomAD database, including 20,387 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 (20383 hom., cov: 32)
  • Exomes 𝑓: 0.46 (4 hom.)
• Consequence: SNX13 ENST00000409604.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.142
• Publications: 43 publications found

Genes affected

SNX13 (HGNC:21335): (sorting nexin 13) This gene encodes a PHOX domain- and RGS domain-containing protein that belongs to the sorting nexin (SNX) family and the regulator of G protein signaling (RGS) family. The PHOX domain is a phosphoinositide binding domain, and the SNX family members are involved in intracellular trafficking. The RGS family members are regulatory molecules that act as GTPase activating proteins for G alpha subunits of heterotrimeric G proteins. The RGS domain of this protein interacts with G alpha(s), accelerates its GTP hydrolysis, and attenuates G alpha(s)-mediated signaling. Overexpression of this protein delayes lysosomal degradation of the epidermal growth factor receptor. Because of its bifunctional role, this protein may link heterotrimeric G protein signaling and vesicular trafficking. [provided by RefSeq, Jul 2008]

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 = 0.707 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000409604.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNX13	NM_015132.5	MANE Select	c.441-3845C>A		intron	N/A	NP_055947.1
	SNX13	NM_001350870.2		c.*3179C>A		3_prime_UTR	Exon 6 of 6	NP_001337799.1
	SNX13	NM_001350862.2		c.441-3845C>A		intron	N/A	NP_001337791.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNX13	ENST00000409604.1	TSL:1	c.*3179C>A		3_prime_UTR	Exon 6 of 6	ENSP00000386639.1
	SNX13	ENST00000428135.7	TSL:1 MANE Select	c.441-3845C>A		intron	N/A	ENSP00000398789.2
	SNX13	ENST00000611725.4	TSL:1	c.441-3845C>A		intron	N/A	ENSP00000479044.1

Frequencies

GnomAD3 genomes AF: 0.497 AC: 75502 AN: 151854 Hom.: 20363 Cov.: 32

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.471

GnomAD4 exome AF: 0.462 AC: 12 AN: 26 Hom.: 4 Cov.: 0 AF XY: 0.500 AC XY: 10 AN XY: 20

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.409 AC: 9 AN: 22

Other (OTH) AF: 1.00 AC: 2 AN: 2

GnomAD4 genome AF: 0.497 AC: 75565 AN: 151972 Hom.: 20383 Cov.: 32 AF XY: 0.490 AC XY: 36416 AN XY: 74276

African (AFR) AF: 0.714 AC: 29605 AN: 41448

American (AMR) AF: 0.471 AC: 7202 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1807 AN: 3472

East Asian (EAS) AF: 0.526 AC: 2708 AN: 5150

South Asian (SAS) AF: 0.457 AC: 2202 AN: 4822

European-Finnish (FIN) AF: 0.296 AC: 3119 AN: 10544

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.404 AC: 27478 AN: 67940

Other (OTH) AF: 0.473 AC: 1000 AN: 2114

Alfa AF: 0.435 Hom.: 23153

Bravo AF: 0.520

Asia WGS AF: 0.514 AC: 1788 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	2.8
DANN	Benign	0.70
PhyloP100		0.14
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: rs4142995; hg19: chr7-17919258;