chr13-42259264-A-G

Variant names:

• chr13-42259264-A-G
• rs2044732

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0361 AC: 1501 AN: 41538

American (AMR) AF: 0.207 AC: 3171 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 411 AN: 3466

East Asian (EAS) AF: 0.0453 AC: 235 AN: 5184

South Asian (SAS) AF: 0.117 AC: 564 AN: 4818

European-Finnish (FIN) AF: 0.251 AC: 2653 AN: 10578

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.217 AC: 14765 AN: 67960

Other (OTH) AF: 0.127 AC: 267 AN: 2108

Alfa AF: 0.190 Hom.: 5169

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
PhyloP100		0.071

Splicing

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

Other links and lift over

dbSNP: rs2044732; hg19: chr13-42833400;