11-57595235-A-G

Variant names:

• chr11-57595235-A-G
• rs2511990

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 0.545 in 151,984 control chromosomes in the GnomAD database, including 23,146 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 (23146 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24
• Publications: 14 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 = 0.828 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82801 AN: 151866 Hom.: 23125 Cov.: 32

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.751

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.850

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.545 AC: 82871 AN: 151984 Hom.: 23146 Cov.: 32 AF XY: 0.554 AC XY: 41133 AN XY: 74296

African (AFR) AF: 0.575 AC: 23839 AN: 41426

American (AMR) AF: 0.589 AC: 9003 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 2155 AN: 3464

East Asian (EAS) AF: 0.849 AC: 4381 AN: 5158

South Asian (SAS) AF: 0.600 AC: 2895 AN: 4824

European-Finnish (FIN) AF: 0.556 AC: 5869 AN: 10554

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.481 AC: 32711 AN: 67968

Other (OTH) AF: 0.542 AC: 1144 AN: 2110

Alfa AF: 0.522 Hom.: 3673

Bravo AF: 0.552

Asia WGS AF: 0.713 AC: 2476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.36
DANN	Benign	0.76
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs2511990; hg19: chr11-57362708;