chr11-76779014-G-A

Variant names:

• chr11-76779014-G-A
• rs1149606

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 0.139 in 152,110 control chromosomes in the GnomAD database, including 1,988 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 0.14 (1988 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21076 AN: 151992 Hom.: 1986 Cov.: 32

Gnomad AFR AF: 0.0393

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.139 AC: 21081 AN: 152110 Hom.: 1988 Cov.: 32 AF XY: 0.141 AC XY: 10511 AN XY: 74356

African (AFR) AF: 0.0393 AC: 1632 AN: 41514

American (AMR) AF: 0.109 AC: 1659 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 570 AN: 3466

East Asian (EAS) AF: 0.401 AC: 2071 AN: 5164

South Asian (SAS) AF: 0.252 AC: 1211 AN: 4806

European-Finnish (FIN) AF: 0.159 AC: 1683 AN: 10584

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11849 AN: 67974

Other (OTH) AF: 0.139 AC: 293 AN: 2110

Alfa AF: 0.158 Hom.: 2286

Bravo AF: 0.131

Asia WGS AF: 0.272 AC: 945 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	14
DANN	Benign	0.68
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs1149606; hg19: chr11-76490058;