rs11961283

Variant names:

• chr6-157977304-T-C
• rs11961283

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 0.334 in 152,086 control chromosomes in the GnomAD database, including 10,124 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 0.33 (10124 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.06
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.559 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: 0.334 AC: 50682 AN: 151966 Hom.: 10108 Cov.: 32

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.334 AC: 50745 AN: 152086 Hom.: 10124 Cov.: 32 AF XY: 0.333 AC XY: 24750 AN XY: 74350

African (AFR) AF: 0.565 AC: 23421 AN: 41444

American (AMR) AF: 0.246 AC: 3753 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 842 AN: 3472

East Asian (EAS) AF: 0.312 AC: 1613 AN: 5164

South Asian (SAS) AF: 0.314 AC: 1514 AN: 4828

European-Finnish (FIN) AF: 0.229 AC: 2424 AN: 10580

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.241 AC: 16352 AN: 67990

Other (OTH) AF: 0.296 AC: 626 AN: 2116

Alfa AF: 0.284 Hom.: 14380

Bravo AF: 0.345

Asia WGS AF: 0.352 AC: 1224 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	0.66
DANN	Benign	0.38
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs11961283; hg19: chr6-158398336;