rs2173746

Variant names:

• chr2-233860084-C-T
• rs2173746

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 0.134 in 151,686 control chromosomes in the GnomAD database, including 1,497 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 0.13 (1497 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.758
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.161 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: 0.134 AC: 20353 AN: 151568 Hom.: 1498 Cov.: 30

Gnomad AFR AF: 0.0894

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.0527

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.134 AC: 20348 AN: 151686 Hom.: 1497 Cov.: 30 AF XY: 0.132 AC XY: 9751 AN XY: 74072

African (AFR) AF: 0.0893 AC: 3697 AN: 41388

American (AMR) AF: 0.125 AC: 1907 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 727 AN: 3460

East Asian (EAS) AF: 0.0526 AC: 270 AN: 5134

South Asian (SAS) AF: 0.126 AC: 604 AN: 4804

European-Finnish (FIN) AF: 0.131 AC: 1373 AN: 10446

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11127 AN: 67922

Other (OTH) AF: 0.146 AC: 309 AN: 2110

Alfa AF: 0.160 Hom.: 2493

Bravo AF: 0.135

Asia WGS AF: 0.0880 AC: 307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.42
DANN	Benign	0.46
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs2173746; hg19: chr2-234768730;