chr11-57592943-A-G

Variant names:

• chr11-57592943-A-G
• rs2729376

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 0.546 in 151,744 control chromosomes in the GnomAD database, including 23,152 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 0.55 (23152 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.173
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.83 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: 0.546 AC: 82764 AN: 151624 Hom.: 23130 Cov.: 31

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.755

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.851

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.640

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.546 AC: 82836 AN: 151744 Hom.: 23152 Cov.: 31 AF XY: 0.554 AC XY: 41115 AN XY: 74156

African (AFR) AF: 0.575 AC: 23809 AN: 41390

American (AMR) AF: 0.590 AC: 8992 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 2160 AN: 3470

East Asian (EAS) AF: 0.851 AC: 4367 AN: 5132

South Asian (SAS) AF: 0.601 AC: 2890 AN: 4808

European-Finnish (FIN) AF: 0.559 AC: 5885 AN: 10530

Middle Eastern (MID) AF: 0.658 AC: 192 AN: 292

European-Non Finnish (NFE) AF: 0.482 AC: 32710 AN: 67870

Other (OTH) AF: 0.545 AC: 1147 AN: 2104

Alfa AF: 0.500 Hom.: 55301

Bravo AF: 0.552

Asia WGS AF: 0.713 AC: 2477 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.1
DANN	Benign	0.84
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs2729376; hg19: chr11-57360416;