rs1214123

Variant names:

• chr2-123940941-A-G
• rs1214123

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 0.418 in 151,890 control chromosomes in the GnomAD database, including 13,461 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 0.42 (13461 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.497
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.445 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: 0.419 AC: 63539 AN: 151772 Hom.: 13461 Cov.: 31

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.418 AC: 63557 AN: 151890 Hom.: 13461 Cov.: 31 AF XY: 0.410 AC XY: 30462 AN XY: 74218

African (AFR) AF: 0.449 AC: 18591 AN: 41412

American (AMR) AF: 0.311 AC: 4746 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1486 AN: 3470

East Asian (EAS) AF: 0.288 AC: 1478 AN: 5136

South Asian (SAS) AF: 0.353 AC: 1702 AN: 4818

European-Finnish (FIN) AF: 0.348 AC: 3664 AN: 10536

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.450 AC: 30547 AN: 67938

Other (OTH) AF: 0.409 AC: 865 AN: 2114

Alfa AF: 0.433 Hom.: 17945

Bravo AF: 0.415

Asia WGS AF: 0.343 AC: 1196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.5
DANN	Benign	0.81
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs1214123; hg19: chr2-124698518;