11-56824969-A-G

Variant names:

• chr11-56824969-A-G
• rs509244

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 0.588 in 152,042 control chromosomes in the GnomAD database, including 26,859 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 0.59 (26859 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.766 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: 0.588 AC: 89360 AN: 151924 Hom.: 26816 Cov.: 32

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.755

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.588 AC: 89466 AN: 152042 Hom.: 26859 Cov.: 32 AF XY: 0.596 AC XY: 44247 AN XY: 74302

African (AFR) AF: 0.654 AC: 27137 AN: 41484

American (AMR) AF: 0.589 AC: 8990 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.521 AC: 1809 AN: 3472

East Asian (EAS) AF: 0.786 AC: 4030 AN: 5128

South Asian (SAS) AF: 0.754 AC: 3638 AN: 4822

European-Finnish (FIN) AF: 0.631 AC: 6675 AN: 10580

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.521 AC: 35393 AN: 67980

Other (OTH) AF: 0.572 AC: 1205 AN: 2106

Alfa AF: 0.531 Hom.: 48088

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.23
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs509244; hg19: chr11-56592445;