rs10427255

Variant names:

• chr2-145367955-C-T
• rs10427255

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 0.548 in 151,888 control chromosomes in the GnomAD database, including 23,038 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 0.55 (23038 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.612 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: 0.548 AC: 83201 AN: 151770 Hom.: 23021 Cov.: 32

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.549

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.548 AC: 83259 AN: 151888 Hom.: 23038 Cov.: 32 AF XY: 0.544 AC XY: 40411 AN XY: 74232

African (AFR) AF: 0.572 AC: 23691 AN: 41434

American (AMR) AF: 0.622 AC: 9483 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2053 AN: 3466

East Asian (EAS) AF: 0.548 AC: 2828 AN: 5158

South Asian (SAS) AF: 0.560 AC: 2687 AN: 4798

European-Finnish (FIN) AF: 0.428 AC: 4510 AN: 10544

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.532 AC: 36149 AN: 67934

Other (OTH) AF: 0.539 AC: 1135 AN: 2104

Alfa AF: 0.545 Hom.: 73569

Bravo AF: 0.563

Asia WGS AF: 0.556 AC: 1928 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.2
DANN	Benign	0.19
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs10427255; hg19: chr2-146125523;