10-62810278-C-T

Variant names:

• chr10-62810278-C-T
• rs10128333

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 0.266 in 152,062 control chromosomes in the GnomAD database, including 6,218 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 0.27 (6218 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.429 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: 0.266 AC: 40347 AN: 151944 Hom.: 6195 Cov.: 33

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.266 AC: 40436 AN: 152062 Hom.: 6218 Cov.: 33 AF XY: 0.270 AC XY: 20095 AN XY: 74326

African (AFR) AF: 0.389 AC: 16113 AN: 41466

American (AMR) AF: 0.344 AC: 5256 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 391 AN: 3470

East Asian (EAS) AF: 0.444 AC: 2292 AN: 5160

South Asian (SAS) AF: 0.324 AC: 1564 AN: 4826

European-Finnish (FIN) AF: 0.232 AC: 2447 AN: 10550

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11587 AN: 67988

Other (OTH) AF: 0.255 AC: 539 AN: 2112

Alfa AF: 0.204 Hom.: 12286

Bravo AF: 0.282

Asia WGS AF: 0.398 AC: 1387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.13
DANN	Benign	0.59
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10128333; hg19: chr10-64570038;