11-57238490-A-G

Position:

• chr11-57238490-A-G

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 0.77 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

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.848

Gnomad4 AMR AF: 0.775

Gnomad4 ASJ AF: 0.764

Gnomad4 EAS AF: 0.775

Gnomad4 SAS AF: 0.799

Gnomad4 FIN AF: 0.796

Gnomad4 NFE AF: 0.717

Gnomad4 OTH AF: 0.767

Alfa AF: 0.728 Hom.: 53533

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7119375; hg19: chr11-57005964;