chr2-126714456-G-A

Variant names:

• chr2-126714456-G-A
• rs2203724

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 0.249 in 152,100 control chromosomes in the GnomAD database, including 5,104 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 0.25 (5104 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.03
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37763 AN: 151982 Hom.: 5091 Cov.: 32

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.0725

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.249 AC: 37810 AN: 152100 Hom.: 5104 Cov.: 32 AF XY: 0.254 AC XY: 18891 AN XY: 74340

African (AFR) AF: 0.197 AC: 8171 AN: 41498

American (AMR) AF: 0.379 AC: 5791 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1033 AN: 3464

East Asian (EAS) AF: 0.457 AC: 2352 AN: 5142

South Asian (SAS) AF: 0.251 AC: 1210 AN: 4816

European-Finnish (FIN) AF: 0.236 AC: 2500 AN: 10586

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 15992 AN: 67984

Other (OTH) AF: 0.286 AC: 603 AN: 2110

Alfa AF: 0.238 Hom.: 2333

Bravo AF: 0.261

Asia WGS AF: 0.369 AC: 1286 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.042
DANN	Benign	0.25
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs2203724; hg19: chr2-127472032;