rs6485963

Variant names:

• chr11-49137671-A-C
• rs6485963

Your query was ambiguous. Multiple possible variants found:

• chr11-49137671-A-C
• chr11-49137671-A-G
• chr11-49137671-A-T

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 0.178 in 151,966 control chromosomes in the GnomAD database, including 2,783 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 0.18 (2783 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.561
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27065 AN: 151852 Hom.: 2782 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.178 AC: 27071 AN: 151966 Hom.: 2783 Cov.: 32 AF XY: 0.181 AC XY: 13438 AN XY: 74250

African (AFR) AF: 0.272 AC: 11253 AN: 41444

American (AMR) AF: 0.132 AC: 2008 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 347 AN: 3464

East Asian (EAS) AF: 0.156 AC: 807 AN: 5166

South Asian (SAS) AF: 0.121 AC: 582 AN: 4820

European-Finnish (FIN) AF: 0.226 AC: 2386 AN: 10542

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9257 AN: 67976

Other (OTH) AF: 0.139 AC: 294 AN: 2110

Alfa AF: 0.127 Hom.: 527

Bravo AF: 0.176

Asia WGS AF: 0.128 AC: 444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.7
DANN	Benign	0.35
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs6485963; hg19: chr11-49159223;