rs2673289

Variant names:

• chr2-147013472-T-C
• rs2673289

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 0.427 in 152,042 control chromosomes in the GnomAD database, including 16,157 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 (16157 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.561 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: 0.427 AC: 64872 AN: 151924 Hom.: 16154 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.427 AC: 64875 AN: 152042 Hom.: 16157 Cov.: 32 AF XY: 0.421 AC XY: 31311 AN XY: 74306

African (AFR) AF: 0.182 AC: 7544 AN: 41518

American (AMR) AF: 0.436 AC: 6653 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.581 AC: 2016 AN: 3470

East Asian (EAS) AF: 0.265 AC: 1369 AN: 5166

South Asian (SAS) AF: 0.445 AC: 2145 AN: 4822

European-Finnish (FIN) AF: 0.466 AC: 4911 AN: 10544

Middle Eastern (MID) AF: 0.500 AC: 145 AN: 290

European-Non Finnish (NFE) AF: 0.566 AC: 38441 AN: 67942

Other (OTH) AF: 0.460 AC: 969 AN: 2108

Alfa AF: 0.487 Hom.: 5187

Bravo AF: 0.412

Asia WGS AF: 0.343 AC: 1193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.45
PhyloP100		0.075

Splicing

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

Other links and lift over

dbSNP: rs2673289; hg19: chr2-147771040;