rs958386

Variant names:

• chr6-156480058-C-T
• rs958386

Variant summary

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

The variant allele was found at a frequency of 0.508 in 151,892 control chromosomes in the GnomAD database, including 23,349 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 0.51 (23349 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.331
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77189 AN: 151784 Hom.: 23347 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.508 AC: 77191 AN: 151892 Hom.: 23349 Cov.: 32 AF XY: 0.505 AC XY: 37501 AN XY: 74240

African (AFR) AF: 0.169 AC: 7007 AN: 41408

American (AMR) AF: 0.572 AC: 8731 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1935 AN: 3470

East Asian (EAS) AF: 0.370 AC: 1914 AN: 5176

South Asian (SAS) AF: 0.471 AC: 2268 AN: 4814

European-Finnish (FIN) AF: 0.665 AC: 6987 AN: 10514

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.684 AC: 46467 AN: 67940

Other (OTH) AF: 0.552 AC: 1160 AN: 2102

Alfa AF: 0.628 Hom.: 128599

Bravo AF: 0.491

Asia WGS AF: 0.376 AC: 1310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	2.5
DANN	Benign	0.73
PhyloP100		-0.33

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs958386; hg19: chr6-156801192;