2-122909495-G-T

Variant names:

• chr2-122909495-G-T
• rs1028184

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 0.408 in 151,640 control chromosomes in the GnomAD database, including 13,425 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 0.41 (13425 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.176
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.561 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: 0.409 AC: 61906 AN: 151522 Hom.: 13423 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.408 AC: 61930 AN: 151640 Hom.: 13425 Cov.: 32 AF XY: 0.414 AC XY: 30677 AN XY: 74052

African (AFR) AF: 0.250 AC: 10348 AN: 41328

American (AMR) AF: 0.497 AC: 7553 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1562 AN: 3464

East Asian (EAS) AF: 0.578 AC: 2964 AN: 5126

South Asian (SAS) AF: 0.562 AC: 2692 AN: 4786

European-Finnish (FIN) AF: 0.460 AC: 4842 AN: 10534

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.448 AC: 30383 AN: 67888

Other (OTH) AF: 0.470 AC: 987 AN: 2098

Alfa AF: 0.418 Hom.: 5716

Bravo AF: 0.403

Asia WGS AF: 0.528 AC: 1834 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.59
DANN	Benign	0.32
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs1028184; hg19: chr2-123667071;