chr17-46935905-T-C

Position:

• chr17-46935905-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000640621.1(GOSR2):​c.*625T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 985,566 control chromosomes in the GnomAD database, including 9,410 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 0.091 (907 hom., cov: 32)
  • Exomes 𝑓: 0.14 (8503 hom.)
• Consequence: GOSR2 ENST00000640621.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20

Genes affected

GOSR2 (HGNC:4431): (golgi SNAP receptor complex member 2) This gene encodes a trafficking membrane protein which transports proteins among the medial- and trans-Golgi compartments. Due to its chromosomal location and trafficking function, this gene may be involved in familial essential hypertension. [provided by RefSeq, Mar 2016]

LRRC37A2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GOSR2	NM_004287.5	c.477+736T>C		intron_variant		ENST00000640051.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GOSR2	ENST00000640051.2	c.477+736T>C		intron_variant		1	NM_004287.5	P3

Frequencies

GnomAD3 genomes AF: 0.0912 AC: 13883 AN: 152154 Hom.: 909 Cov.: 32

Gnomad AFR AF: 0.0228

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.0754

Gnomad ASJ AF: 0.0507

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0391

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.0952

GnomAD4 exome AF: 0.139 AC: 115622 AN: 833294 Hom.: 8503 Cov.: 29 AF XY: 0.139 AC XY: 53510 AN XY: 384876

Gnomad4 AFR exome AF: 0.0132

Gnomad4 AMR exome AF: 0.0709

Gnomad4 ASJ exome AF: 0.0528

Gnomad4 EAS exome AF: 0.00138

Gnomad4 SAS exome AF: 0.0394

Gnomad4 FIN exome AF: 0.195

Gnomad4 NFE exome AF: 0.146

Gnomad4 OTH exome AF: 0.115

GnomAD4 genome AF: 0.0911 AC: 13876 AN: 152272 Hom.: 907 Cov.: 32 AF XY: 0.0903 AC XY: 6725 AN XY: 74456

Gnomad4 AFR AF: 0.0227

Gnomad4 AMR AF: 0.0753

Gnomad4 ASJ AF: 0.0507

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0392

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.0942

Alfa AF: 0.120 Hom.: 2820

Bravo AF: 0.0819

Asia WGS AF: 0.0180 AC: 63 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	18
DANN	Benign	0.79

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs17608766; hg19: chr17-45013271;