11-56824969-A-T

Variant names:

• chr11-56824969-A-T
• 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 0.0632 in 152,094 control chromosomes in the GnomAD database, including 440 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 0.063 (440 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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0873 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: 0.0633 AC: 9613 AN: 151976 Hom.: 438 Cov.: 32

Gnomad AFR AF: 0.0176

Gnomad AMI AF: 0.0474

Gnomad AMR AF: 0.0583

Gnomad ASJ AF: 0.0291

Gnomad EAS AF: 0.000583

Gnomad SAS AF: 0.0586

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0892

Gnomad OTH AF: 0.0713

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

GnomAD4 genome AF: 0.0632 AC: 9615 AN: 152094 Hom.: 440 Cov.: 32 AF XY: 0.0639 AC XY: 4748 AN XY: 74334

African (AFR) AF: 0.0176 AC: 730 AN: 41500

American (AMR) AF: 0.0582 AC: 889 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0291 AC: 101 AN: 3472

East Asian (EAS) AF: 0.000585 AC: 3 AN: 5130

South Asian (SAS) AF: 0.0591 AC: 285 AN: 4826

European-Finnish (FIN) AF: 0.126 AC: 1336 AN: 10584

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0892 AC: 6062 AN: 67996

Other (OTH) AF: 0.0710 AC: 150 AN: 2112

Alfa AF: 0.00143 Hom.: 48088

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.15
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;