6-151655950-G-A

Variant names:

• chr6-151655950-G-A
• rs6915267

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 0.157 in 151,960 control chromosomes in the GnomAD database, including 2,776 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 0.16 (2776 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.309
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23883 AN: 151842 Hom.: 2773 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0333

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0856

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.157 AC: 23903 AN: 151960 Hom.: 2776 Cov.: 32 AF XY: 0.153 AC XY: 11330 AN XY: 74280

African (AFR) AF: 0.323 AC: 13363 AN: 41424

American (AMR) AF: 0.103 AC: 1568 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 349 AN: 3470

East Asian (EAS) AF: 0.287 AC: 1479 AN: 5160

South Asian (SAS) AF: 0.113 AC: 547 AN: 4822

European-Finnish (FIN) AF: 0.0333 AC: 352 AN: 10568

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0855 AC: 5809 AN: 67928

Other (OTH) AF: 0.159 AC: 335 AN: 2110

Alfa AF: 0.125 Hom.: 267

Bravo AF: 0.170

Asia WGS AF: 0.205 AC: 709 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
DANN	Benign	0.66
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs6915267; hg19: chr6-151977085;