2-125530483-T-C

Variant names:

• chr2-125530483-T-C
• rs6710520

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 0.23 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
• Publications: 1 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 = 0.847 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

African (AFR) AF: 0.315 AC: 13061 AN: 41464

American (AMR) AF: 0.342 AC: 5226 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 722 AN: 3468

East Asian (EAS) AF: 0.868 AC: 4485 AN: 5168

South Asian (SAS) AF: 0.439 AC: 2118 AN: 4822

European-Finnish (FIN) AF: 0.113 AC: 1199 AN: 10594

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7514 AN: 67984

Other (OTH) AF: 0.238 AC: 503 AN: 2112

Alfa AF: 0.149 Hom.: 1468

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
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs6710520; hg19: chr2-126288060;