11-57238490-A-G

Variant names:

• chr11-57238490-A-G
• rs7119375

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 0.77 in 152,156 control chromosomes in the GnomAD database, including 45,490 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 0.77 (45490 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.535
• Publications: 25 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.841 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: 0.770 AC: 117114 AN: 152038 Hom.: 45435 Cov.: 32

Gnomad AFR AF: 0.848

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.775

Gnomad ASJ AF: 0.764

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.800

Gnomad FIN AF: 0.796

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.770 AC: 117233 AN: 152156 Hom.: 45490 Cov.: 32 AF XY: 0.774 AC XY: 57565 AN XY: 74368

African (AFR) AF: 0.848 AC: 35214 AN: 41510

American (AMR) AF: 0.775 AC: 11836 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.764 AC: 2653 AN: 3472

East Asian (EAS) AF: 0.775 AC: 4013 AN: 5178

South Asian (SAS) AF: 0.799 AC: 3863 AN: 4832

European-Finnish (FIN) AF: 0.796 AC: 8420 AN: 10582

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.717 AC: 48746 AN: 67990

Other (OTH) AF: 0.767 AC: 1622 AN: 2114

Alfa AF: 0.734 Hom.: 75511

Bravo AF: 0.768

Asia WGS AF: 0.832 AC: 2891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.56
DANN	Benign	0.53
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs7119375; hg19: chr11-57005964;