rs958386

chr6-156480058-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.572

Gnomad4 ASJ AF: 0.558

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.665

Gnomad4 NFE AF: 0.684

Gnomad4 OTH AF: 0.552

Alfa AF: 0.646 Hom.: 65984

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs958386; hg19: chr6-156801192;