11-94957424-G-C

Variant names:

• chr11-94957424-G-C
• rs923190

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 0.94 in 152,228 control chromosomes in the GnomAD database, including 67,673 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 0.94 (67673 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.869
• Publications: 0 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 (EAS) allele frequency at 95% confidence interval = 0.98 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: 0.940 AC: 143032 AN: 152110 Hom.: 67626 Cov.: 31

Gnomad AFR AF: 0.824

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.976

Gnomad ASJ AF: 0.963

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.954

Gnomad FIN AF: 0.996

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.987

Gnomad OTH AF: 0.956

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

GnomAD4 genome AF: 0.940 AC: 143137 AN: 152228 Hom.: 67673 Cov.: 31 AF XY: 0.942 AC XY: 70087 AN XY: 74434

African (AFR) AF: 0.824 AC: 34175 AN: 41490

American (AMR) AF: 0.976 AC: 14930 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.963 AC: 3343 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5174 AN: 5178

South Asian (SAS) AF: 0.955 AC: 4597 AN: 4816

European-Finnish (FIN) AF: 0.996 AC: 10570 AN: 10616

Middle Eastern (MID) AF: 0.980 AC: 288 AN: 294

European-Non Finnish (NFE) AF: 0.987 AC: 67127 AN: 68036

Other (OTH) AF: 0.956 AC: 2021 AN: 2114

Alfa AF: 0.959 Hom.: 8721

Bravo AF: 0.934

Asia WGS AF: 0.973 AC: 3384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.037
DANN	Benign	0.44
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs923190; hg19: chr11-94690589;