rs2203724

Positions:

• chr2-126714456-G-A
• chr2-126714456-G-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.235

Gnomad4 OTH AF: 0.286

Alfa AF: 0.238 Hom.: 2077

Bravo AF: 0.261

Asia WGS AF: 0.369 AC: 1286 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2203724; hg19: chr2-127472032;