chr11-57595330-G-A

Position:

• chr11-57595330-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0862

Gnomad4 AMR AF: 0.0661

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.0578

Gnomad4 NFE AF: 0.0980

Gnomad4 OTH AF: 0.0948

Alfa AF: 0.0954 Hom.: 983

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3758919; hg19: chr11-57362803;