11-128874308-G-A

Variant names:

• chr11-128874308-G-A
• rs948215

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 0.667 in 151,902 control chromosomes in the GnomAD database, including 34,591 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 0.67 (34591 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.859 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: 0.667 AC: 101271 AN: 151784 Hom.: 34579 Cov.: 30

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.782

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.881

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.732

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.667 AC: 101319 AN: 151902 Hom.: 34591 Cov.: 30 AF XY: 0.673 AC XY: 49954 AN XY: 74258

African (AFR) AF: 0.518 AC: 21406 AN: 41364

American (AMR) AF: 0.782 AC: 11937 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.688 AC: 2387 AN: 3470

East Asian (EAS) AF: 0.880 AC: 4546 AN: 5164

South Asian (SAS) AF: 0.590 AC: 2839 AN: 4810

European-Finnish (FIN) AF: 0.748 AC: 7908 AN: 10566

Middle Eastern (MID) AF: 0.736 AC: 215 AN: 292

European-Non Finnish (NFE) AF: 0.705 AC: 47900 AN: 67952

Other (OTH) AF: 0.696 AC: 1471 AN: 2112

Alfa AF: 0.696 Hom.: 60827

Bravo AF: 0.666

Asia WGS AF: 0.743 AC: 2588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.023
DANN	Benign	0.38
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs948215; hg19: chr11-128744203;