rs938595

Variant names:

• chr11-102545128-G-A
• rs938595

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 0.533 in 152,138 control chromosomes in the GnomAD database, including 21,728 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 0.53 (21728 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.539

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.55 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: 0.533 AC: 81090 AN: 152022 Hom.: 21707 Cov.: 33

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.533 AC: 81164 AN: 152138 Hom.: 21728 Cov.: 33 AF XY: 0.530 AC XY: 39445 AN XY: 74356

Gnomad4 AFR AF: 0.517

Gnomad4 AMR AF: 0.523

Gnomad4 ASJ AF: 0.512

Gnomad4 EAS AF: 0.483

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.554

Gnomad4 NFE AF: 0.555

Gnomad4 OTH AF: 0.505

Alfa AF: 0.538 Hom.: 12589

Bravo AF: 0.533

Asia WGS AF: 0.409 AC: 1421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs938595; hg19: chr11-102415859;