2-125530483-T-C

Variant names:

• chr2-125530483-T-C
• rs6710520

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 0.23 in 152,096 control chromosomes in the GnomAD database, including 6,217 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 0.23 (6217 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90

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 = 0.847 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: 0.230 AC: 34913 AN: 151976 Hom.: 6198 Cov.: 33

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.869

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.230 AC: 34975 AN: 152096 Hom.: 6217 Cov.: 33 AF XY: 0.240 AC XY: 17886 AN XY: 74376

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.868

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.238

Alfa AF: 0.150 Hom.: 1345

Bravo AF: 0.253

Asia WGS AF: 0.651 AC: 2260 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	0.56
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6710520; hg19: chr2-126288060;