rs2419976

Variant names:

• chr2-123522573-T-C
• rs2419976

Your query was ambiguous. Multiple possible variants found:

• chr2-123522573-T-C
• chr2-123522573-T-G

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 0.125 in 152,120 control chromosomes in the GnomAD database, including 1,434 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 (1434 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.103
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.343 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: 0.125 AC: 18982 AN: 152002 Hom.: 1434 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.125 AC: 18989 AN: 152120 Hom.: 1434 Cov.: 32 AF XY: 0.129 AC XY: 9598 AN XY: 74368

African (AFR) AF: 0.101 AC: 4175 AN: 41522

American (AMR) AF: 0.159 AC: 2429 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 551 AN: 3470

East Asian (EAS) AF: 0.357 AC: 1840 AN: 5154

South Asian (SAS) AF: 0.180 AC: 867 AN: 4816

European-Finnish (FIN) AF: 0.127 AC: 1348 AN: 10584

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7350 AN: 67980

Other (OTH) AF: 0.162 AC: 341 AN: 2110

Alfa AF: 0.121 Hom.: 2004

Bravo AF: 0.126

Asia WGS AF: 0.216 AC: 748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.76
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs2419976; hg19: chr2-124280149;