chr2-102399227-C-T

Variant names:

• chr2-102399227-C-T
• rs1420094

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 0.535 in 152,080 control chromosomes in the GnomAD database, including 23,625 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 (23625 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.958
• Publications: 19 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 = 0.726 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: 0.535 AC: 81272 AN: 151962 Hom.: 23594 Cov.: 33

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.535 AC: 81356 AN: 152080 Hom.: 23625 Cov.: 33 AF XY: 0.529 AC XY: 39323 AN XY: 74354

African (AFR) AF: 0.733 AC: 30394 AN: 41492

American (AMR) AF: 0.414 AC: 6336 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2133 AN: 3472

East Asian (EAS) AF: 0.150 AC: 775 AN: 5180

South Asian (SAS) AF: 0.265 AC: 1278 AN: 4822

European-Finnish (FIN) AF: 0.543 AC: 5741 AN: 10576

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.486 AC: 33016 AN: 67944

Other (OTH) AF: 0.520 AC: 1095 AN: 2104

Alfa AF: 0.487 Hom.: 9780

Bravo AF: 0.536

Asia WGS AF: 0.232 AC: 809 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	0.64
DANN	Benign	0.47
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs1420094; hg19: chr2-103015687; COSMIC: COSV52123631;