2-187629269-C-T

Variant names:

• chr2-187629269-C-T
• rs1464337

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 0.122 in 152,052 control chromosomes in the GnomAD database, including 1,902 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 0.12 (1902 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.09).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.271 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: 0.122 AC: 18569 AN: 151934 Hom.: 1894 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.0736

Gnomad EAS AF: 0.0174

Gnomad SAS AF: 0.0510

Gnomad FIN AF: 0.0263

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0579

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.122 AC: 18613 AN: 152052 Hom.: 1902 Cov.: 32 AF XY: 0.120 AC XY: 8937 AN XY: 74338

African (AFR) AF: 0.275 AC: 11407 AN: 41434

American (AMR) AF: 0.139 AC: 2116 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0736 AC: 255 AN: 3464

East Asian (EAS) AF: 0.0174 AC: 90 AN: 5164

South Asian (SAS) AF: 0.0508 AC: 245 AN: 4822

European-Finnish (FIN) AF: 0.0263 AC: 278 AN: 10586

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0579 AC: 3936 AN: 67994

Other (OTH) AF: 0.117 AC: 246 AN: 2108

Alfa AF: 0.0327 Hom.: 46

Bravo AF: 0.139

Asia WGS AF: 0.0630 AC: 220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.52
DANN	Benign	0.82
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1464337; hg19: chr2-188493996;