rs2038946

Positions:

• chr13-74547065-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 0.43 in 151,924 control chromosomes in the GnomAD database, including 15,708 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 0.43 (15708 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128

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 (EAS) allele frequency at 95% confidence interval = 0.731 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: 0.430 AC: 65331 AN: 151806 Hom.: 15702 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.430 AC: 65353 AN: 151924 Hom.: 15708 Cov.: 32 AF XY: 0.430 AC XY: 31953 AN XY: 74250

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.751

Gnomad4 SAS AF: 0.534

Gnomad4 FIN AF: 0.492

Gnomad4 NFE AF: 0.529

Gnomad4 OTH AF: 0.426

Alfa AF: 0.512 Hom.: 10881

Bravo AF: 0.415

Asia WGS AF: 0.576 AC: 1975 AN: 3430

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.35
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2038946; hg19: chr13-75121202;