rs2673289

chr2-147013472-T-C

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 0.427 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.436

Gnomad4 ASJ AF: 0.581

Gnomad4 EAS AF: 0.265

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.466

Gnomad4 NFE AF: 0.566

Gnomad4 OTH AF: 0.460

Alfa AF: 0.458 Hom.: 2749

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2673289; hg19: chr2-147771040;