rs2044732

Variant names:

• chr13-42259264-A-G
• rs2044732

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 0.156 in 152,140 control chromosomes in the GnomAD database, including 2,477 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 0.16 (2477 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.214 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: 0.156 AC: 23786 AN: 152022 Hom.: 2471 Cov.: 31

Gnomad AFR AF: 0.0362

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.0452

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.156 AC: 23797 AN: 152140 Hom.: 2477 Cov.: 31 AF XY: 0.158 AC XY: 11734 AN XY: 74390

Gnomad4 AFR AF: 0.0361

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.0453

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.127

Alfa AF: 0.195 Hom.: 4174

Bravo AF: 0.147

Asia WGS AF: 0.0740 AC: 258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.5
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2044732; hg19: chr13-42833400;