rs4963049

Variant names:

• chr11-1215197-G-A
• rs4963049

Your query was ambiguous. Multiple possible variants found:

• chr11-1215197-G-A
• chr11-1215197-G-C
• chr11-1215197-G-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 0.924 in 152,320 control chromosomes in the GnomAD database, including 65,154 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 0.92 (65154 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.924 AC: 140578 AN: 152202 Hom.: 65091 Cov.: 33

Gnomad AFR AF: 0.980

Gnomad AMI AF: 0.899

Gnomad AMR AF: 0.940

Gnomad ASJ AF: 0.853

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.893

Gnomad FIN AF: 0.924

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.886

Gnomad OTH AF: 0.922

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

GnomAD4 genome AF: 0.924 AC: 140700 AN: 152320 Hom.: 65154 Cov.: 33 AF XY: 0.925 AC XY: 68915 AN XY: 74472

African (AFR) AF: 0.980 AC: 40762 AN: 41582

American (AMR) AF: 0.940 AC: 14384 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.853 AC: 2962 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5173 AN: 5182

South Asian (SAS) AF: 0.892 AC: 4305 AN: 4826

European-Finnish (FIN) AF: 0.924 AC: 9807 AN: 10610

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.886 AC: 60270 AN: 68026

Other (OTH) AF: 0.923 AC: 1950 AN: 2112

Alfa AF: 0.926 Hom.: 22277

Bravo AF: 0.929

Asia WGS AF: 0.965 AC: 3355 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.84
DANN	Benign	0.22
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs4963049; hg19: chr11-1236427;