rs1938651

chr11-58345478-C-T

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 0.715 in 151,800 control chromosomes in the GnomAD database, including 39,464 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 0.72 (39464 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.715 AC: 108465 AN: 151680 Hom.: 39411 Cov.: 31

Gnomad AFR AF: 0.844

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.752

Gnomad ASJ AF: 0.653

Gnomad EAS AF: 0.854

Gnomad SAS AF: 0.696

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.725

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

GnomAD4 genome AF: 0.715 AC: 108579 AN: 151800 Hom.: 39464 Cov.: 31 AF XY: 0.718 AC XY: 53270 AN XY: 74194

Gnomad4 AFR AF: 0.844

Gnomad4 AMR AF: 0.752

Gnomad4 ASJ AF: 0.653

Gnomad4 EAS AF: 0.854

Gnomad4 SAS AF: 0.696

Gnomad4 FIN AF: 0.662

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.726

Alfa AF: 0.650 Hom.: 42402

Bravo AF: 0.730

Asia WGS AF: 0.743 AC: 2584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.6
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1938651; hg19: chr11-58112951;