rs13010671

Variant names:

• chr2-161028581-C-T
• rs13010671

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 0.149 in 152,118 control chromosomes in the GnomAD database, including 1,960 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 0.15 (1960 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.917
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.236 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: 0.149 AC: 22594 AN: 152000 Hom.: 1952 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.00385

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.149 AC: 22627 AN: 152118 Hom.: 1960 Cov.: 32 AF XY: 0.149 AC XY: 11054 AN XY: 74354

African (AFR) AF: 0.239 AC: 9929 AN: 41466

American (AMR) AF: 0.117 AC: 1788 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 549 AN: 3472

East Asian (EAS) AF: 0.00386 AC: 20 AN: 5182

South Asian (SAS) AF: 0.133 AC: 643 AN: 4822

European-Finnish (FIN) AF: 0.141 AC: 1491 AN: 10584

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7558 AN: 67998

Other (OTH) AF: 0.163 AC: 344 AN: 2110

Alfa AF: 0.129 Hom.: 252

Bravo AF: 0.149

Asia WGS AF: 0.0840 AC: 294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.67
DANN	Benign	0.19
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs13010671; hg19: chr2-161885092;