rs1938651

Variant names:

• chr11-58345478-C-T
• rs1938651

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 0.715 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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.844 AC: 34972 AN: 41442

American (AMR) AF: 0.752 AC: 11446 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.653 AC: 2265 AN: 3470

East Asian (EAS) AF: 0.854 AC: 4377 AN: 5128

South Asian (SAS) AF: 0.696 AC: 3340 AN: 4802

European-Finnish (FIN) AF: 0.662 AC: 6977 AN: 10546

Middle Eastern (MID) AF: 0.652 AC: 189 AN: 290

European-Non Finnish (NFE) AF: 0.631 AC: 42865 AN: 67886

Other (OTH) AF: 0.726 AC: 1529 AN: 2106

Alfa AF: 0.658 Hom.: 55109

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
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs1938651; hg19: chr11-58112951;