6-132571801-A-G

Variant names:

• chr6-132571801-A-G
• rs11154685

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 0.309 in 151,374 control chromosomes in the GnomAD database, including 7,372 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 0.31 (7372 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.348
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.446 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: 0.309 AC: 46759 AN: 151256 Hom.: 7366 Cov.: 31

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.309 AC: 46797 AN: 151374 Hom.: 7372 Cov.: 31 AF XY: 0.314 AC XY: 23183 AN XY: 73936

African (AFR) AF: 0.240 AC: 9876 AN: 41174

American (AMR) AF: 0.379 AC: 5748 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1090 AN: 3470

East Asian (EAS) AF: 0.343 AC: 1767 AN: 5150

South Asian (SAS) AF: 0.462 AC: 2223 AN: 4812

European-Finnish (FIN) AF: 0.358 AC: 3725 AN: 10418

Middle Eastern (MID) AF: 0.395 AC: 113 AN: 286

European-Non Finnish (NFE) AF: 0.312 AC: 21181 AN: 67866

Other (OTH) AF: 0.340 AC: 717 AN: 2106

Alfa AF: 0.304 Hom.: 7475

Bravo AF: 0.308

Asia WGS AF: 0.398 AC: 1380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.1
DANN	Benign	0.75
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs11154685; hg19: chr6-132892940; COSMIC: COSV51582585;