6-160316549-C-A

Variant names:

• chr6-160316549-C-A
• rs446809

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 0.617 in 151,986 control chromosomes in the GnomAD database, including 29,217 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 0.62 (29217 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.673 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: 0.617 AC: 93697 AN: 151868 Hom.: 29193 Cov.: 32

Gnomad AFR AF: 0.588

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.618

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.617 AC: 93766 AN: 151986 Hom.: 29217 Cov.: 32 AF XY: 0.611 AC XY: 45413 AN XY: 74268

African (AFR) AF: 0.588 AC: 24354 AN: 41418

American (AMR) AF: 0.524 AC: 8001 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2111 AN: 3468

East Asian (EAS) AF: 0.422 AC: 2180 AN: 5166

South Asian (SAS) AF: 0.479 AC: 2312 AN: 4830

European-Finnish (FIN) AF: 0.640 AC: 6757 AN: 10562

Middle Eastern (MID) AF: 0.610 AC: 178 AN: 292

European-Non Finnish (NFE) AF: 0.678 AC: 46068 AN: 67970

Other (OTH) AF: 0.619 AC: 1306 AN: 2110

Alfa AF: 0.629 Hom.: 5303

Bravo AF: 0.610

Asia WGS AF: 0.451 AC: 1570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.94
DANN	Benign	0.29
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs446809; hg19: chr6-160737581;