chr6-169256153-A-G

Variant names:

• chr6-169256153-A-G
• rs6605523

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 0.412 in 152,150 control chromosomes in the GnomAD database, including 13,881 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 0.41 (13881 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.267
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62710 AN: 152032 Hom.: 13873 Cov.: 34

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.834

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.412 AC: 62753 AN: 152150 Hom.: 13881 Cov.: 34 AF XY: 0.421 AC XY: 31331 AN XY: 74424

African (AFR) AF: 0.387 AC: 16042 AN: 41498

American (AMR) AF: 0.550 AC: 8414 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1247 AN: 3472

East Asian (EAS) AF: 0.834 AC: 4300 AN: 5158

South Asian (SAS) AF: 0.535 AC: 2577 AN: 4816

European-Finnish (FIN) AF: 0.401 AC: 4252 AN: 10608

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.361 AC: 24534 AN: 67996

Other (OTH) AF: 0.409 AC: 862 AN: 2110

Alfa AF: 0.382 Hom.: 21575

Bravo AF: 0.422

Asia WGS AF: 0.677 AC: 2352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.70
DANN	Benign	0.52
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs6605523; hg19: chr6-169656248;