2-129240870-T-C

Variant names:

• chr2-129240870-T-C
• rs2952621

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 0.532 in 151,942 control chromosomes in the GnomAD database, including 21,899 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 0.53 (21899 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.224
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.614 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: 0.532 AC: 80720 AN: 151822 Hom.: 21864 Cov.: 32

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.539

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.532 AC: 80809 AN: 151942 Hom.: 21899 Cov.: 32 AF XY: 0.524 AC XY: 38928 AN XY: 74250

African (AFR) AF: 0.620 AC: 25680 AN: 41422

American (AMR) AF: 0.473 AC: 7225 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.589 AC: 2044 AN: 3468

East Asian (EAS) AF: 0.229 AC: 1177 AN: 5138

South Asian (SAS) AF: 0.435 AC: 2097 AN: 4822

European-Finnish (FIN) AF: 0.464 AC: 4890 AN: 10548

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.528 AC: 35896 AN: 67950

Other (OTH) AF: 0.535 AC: 1129 AN: 2110

Alfa AF: 0.531 Hom.: 57966

Bravo AF: 0.536

Asia WGS AF: 0.366 AC: 1274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.63
DANN	Benign	0.23
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs2952621; hg19: chr2-129998443;