rs2755238

chr13-40536133-T-C

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 0.079 in 152,246 control chromosomes in the GnomAD database, including 568 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 0.079 (568 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0977 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: 0.0790 AC: 12024 AN: 152128 Hom.: 567 Cov.: 32

Gnomad AFR AF: 0.0466

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.0982

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0422

Gnomad FIN AF: 0.0702

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.0997

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.0790 AC: 12026 AN: 152246 Hom.: 568 Cov.: 32 AF XY: 0.0754 AC XY: 5611 AN XY: 74436

Gnomad4 AFR AF: 0.0466

Gnomad4 AMR AF: 0.0980

Gnomad4 ASJ AF: 0.111

Gnomad4 EAS AF: 0.000385

Gnomad4 SAS AF: 0.0416

Gnomad4 FIN AF: 0.0702

Gnomad4 NFE AF: 0.0997

Gnomad4 OTH AF: 0.120

Alfa AF: 0.0901 Hom.: 170

Bravo AF: 0.0803

Asia WGS AF: 0.0210 AC: 74 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.10
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2755238; hg19: chr13-41110270;