2-238955452-C-T

Variant names:

• chr2-238955452-C-T
• rs12477314

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 0.151 in 152,164 control chromosomes in the GnomAD database, including 2,267 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 (2267 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.388
• Publications: 46 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.246 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: 0.152 AC: 23039 AN: 152046 Hom.: 2267 Cov.: 32

Gnomad AFR AF: 0.0371

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.151 AC: 23032 AN: 152164 Hom.: 2267 Cov.: 32 AF XY: 0.151 AC XY: 11254 AN XY: 74376

African (AFR) AF: 0.0369 AC: 1534 AN: 41536

American (AMR) AF: 0.134 AC: 2054 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 767 AN: 3468

East Asian (EAS) AF: 0.258 AC: 1332 AN: 5168

South Asian (SAS) AF: 0.111 AC: 537 AN: 4830

European-Finnish (FIN) AF: 0.209 AC: 2210 AN: 10562

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14049 AN: 67996

Other (OTH) AF: 0.165 AC: 349 AN: 2110

Alfa AF: 0.187 Hom.: 8032

Bravo AF: 0.143

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.98
DANN	Benign	0.89
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs12477314; hg19: chr2-239877148;