chr11-57242124-C-A

Variant names:

• chr11-57242124-C-A
• rs948844

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 0.581 in 151,976 control chromosomes in the GnomAD database, including 26,024 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 0.58 (26024 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.60
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.695 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: 0.581 AC: 88213 AN: 151858 Hom.: 26000 Cov.: 32

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.581 AC: 88295 AN: 151976 Hom.: 26024 Cov.: 32 AF XY: 0.590 AC XY: 43793 AN XY: 74250

African (AFR) AF: 0.506 AC: 20961 AN: 41428

American (AMR) AF: 0.643 AC: 9833 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2286 AN: 3468

East Asian (EAS) AF: 0.712 AC: 3668 AN: 5154

South Asian (SAS) AF: 0.715 AC: 3445 AN: 4818

European-Finnish (FIN) AF: 0.672 AC: 7102 AN: 10562

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.574 AC: 39000 AN: 67942

Other (OTH) AF: 0.616 AC: 1298 AN: 2108

Alfa AF: 0.575 Hom.: 4343

Bravo AF: 0.573

Asia WGS AF: 0.738 AC: 2567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.9
DANN	Benign	0.55
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs948844; hg19: chr11-57009598;