chr11-57595330-G-A

Variant names:

• chr11-57595330-G-A
• rs3758919

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 0.0905 in 152,194 control chromosomes in the GnomAD database, including 658 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 0.091 (658 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.112 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: 0.0905 AC: 13770 AN: 152076 Hom.: 656 Cov.: 33

Gnomad AFR AF: 0.0864

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.0662

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0578

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0980

Gnomad OTH AF: 0.0934

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

GnomAD4 genome AF: 0.0905 AC: 13776 AN: 152194 Hom.: 658 Cov.: 33 AF XY: 0.0904 AC XY: 6725 AN XY: 74430

African (AFR) AF: 0.0862 AC: 3580 AN: 41510

American (AMR) AF: 0.0661 AC: 1010 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 474 AN: 3472

East Asian (EAS) AF: 0.104 AC: 540 AN: 5184

South Asian (SAS) AF: 0.120 AC: 582 AN: 4830

European-Finnish (FIN) AF: 0.0578 AC: 613 AN: 10598

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.0980 AC: 6666 AN: 68008

Other (OTH) AF: 0.0948 AC: 200 AN: 2110

Alfa AF: 0.0942 Hom.: 1242

Bravo AF: 0.0893

Asia WGS AF: 0.115 AC: 400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	2.2
DANN	Benign	0.72
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs3758919; hg19: chr11-57362803;