rs2044732

Positions:

• chr13-42259264-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 0.156 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;