rs4673546

Variant names:

• chr2-210700968-C-T
• rs4673546

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 0.155 in 152,148 control chromosomes in the GnomAD database, including 2,298 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 (2298 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.197 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: 0.155 AC: 23584 AN: 152030 Hom.: 2295 Cov.: 32

Gnomad AFR AF: 0.0350

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.155 AC: 23583 AN: 152148 Hom.: 2298 Cov.: 32 AF XY: 0.162 AC XY: 12018 AN XY: 74380

African (AFR) AF: 0.0348 AC: 1448 AN: 41552

American (AMR) AF: 0.203 AC: 3096 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 568 AN: 3472

East Asian (EAS) AF: 0.158 AC: 817 AN: 5158

South Asian (SAS) AF: 0.184 AC: 890 AN: 4832

European-Finnish (FIN) AF: 0.303 AC: 3203 AN: 10574

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.192 AC: 13043 AN: 67968

Other (OTH) AF: 0.144 AC: 305 AN: 2114

Alfa AF: 0.170 Hom.: 6554

Bravo AF: 0.143

Asia WGS AF: 0.167 AC: 584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.86
DANN	Benign	0.55
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4673546; hg19: chr2-211565692;