NM_015132.5:c.1954-9delT

Variant names:

• chr7-17814952-GA-G
• rs34649849
• NM_015132.5:c.1954-9delT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_015132.5(SNX13):​c.1954-9delT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0022 (0 hom., cov: 0)
  • Exomes 𝑓: 0.034 (0 hom.)
• Consequence: SNX13 NM_015132.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.43

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

Verdict is Benign. Variant got -8 ACMG points.

• BS1: Variant frequency is greater than expected in population amr. gnomad4_exome allele frequency = 0.0337 (35034/1040898) while in subpopulation AMR AF= 0.0462 (433/9380). AF 95% confidence interval is 0.0426. There are 0 homozygotes in gnomad4_exome. There are 17281 alleles in male gnomad4_exome subpopulation. Median coverage is 12. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 290 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNX13	NM_015132.5	c.1954-9delT		intron_variant	Intron 19 of 25	ENST00000428135.7	NP_055947.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNX13	ENST00000428135.7	c.1954-9delT		intron_variant	Intron 19 of 25	1	NM_015132.5	ENSP00000398789.2
SNX13	ENST00000611725.4	c.1987-9delT		intron_variant	Intron 19 of 24	1		ENSP00000479044.1
SNX13	ENST00000496855.1	n.298-9delT		intron_variant	Intron 2 of 8	1
SNX13	ENST00000409076.6	n.*1652-9delT		intron_variant	Intron 20 of 26	2		ENSP00000387053.2

Frequencies

GnomAD3 genomes AF: 0.00217 AC: 283 AN: 130306 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00561

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00186

Gnomad ASJ AF: 0.000317

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000231

Gnomad FIN AF: 0.00325

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000502

Gnomad OTH AF: 0.00113

GnomAD3 exomes AF: 0.0894 AC: 3050 AN: 34130 Hom.: 0 AF XY: 0.0886 AC XY: 1689 AN XY: 19058

Gnomad AFR exome AF: 0.0306

Gnomad AMR exome AF: 0.0990

Gnomad ASJ exome AF: 0.101

Gnomad EAS exome AF: 0.0643

Gnomad SAS exome AF: 0.0732

Gnomad FIN exome AF: 0.110

Gnomad NFE exome AF: 0.0911

Gnomad OTH exome AF: 0.103

GnomAD4 exome AF: 0.0337 AC: 35034 AN: 1040898 Hom.: 0 Cov.: 12 AF XY: 0.0341 AC XY: 17281 AN XY: 506294

Gnomad4 AFR exome AF: 0.0120

Gnomad4 AMR exome AF: 0.0462

Gnomad4 ASJ exome AF: 0.0461

Gnomad4 EAS exome AF: 0.0202

Gnomad4 SAS exome AF: 0.0360

Gnomad4 FIN exome AF: 0.0720

Gnomad4 NFE exome AF: 0.0328

Gnomad4 OTH exome AF: 0.0338

GnomAD4 genome AF: 0.00223 AC: 290 AN: 130320 Hom.: 0 Cov.: 0 AF XY: 0.00234 AC XY: 146 AN XY: 62462

Gnomad4 AFR AF: 0.00579

Gnomad4 AMR AF: 0.00186

Gnomad4 ASJ AF: 0.000317

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000233

Gnomad4 FIN AF: 0.00325

Gnomad4 NFE AF: 0.000502

Gnomad4 OTH AF: 0.00112

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs34649849; hg19: chr7-17854575;