rs10465850

Variant names:

• chr1-65233520-C-T
• rs10465850

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 0.387 in 151,830 control chromosomes in the GnomAD database, including 11,510 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 0.39 (11510 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.43 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: 0.387 AC: 58665 AN: 151712 Hom.: 11508 Cov.: 31

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.387 AC: 58702 AN: 151830 Hom.: 11510 Cov.: 31 AF XY: 0.378 AC XY: 28065 AN XY: 74174

African (AFR) AF: 0.365 AC: 15093 AN: 41386

American (AMR) AF: 0.353 AC: 5387 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1377 AN: 3464

East Asian (EAS) AF: 0.314 AC: 1616 AN: 5148

South Asian (SAS) AF: 0.354 AC: 1703 AN: 4814

European-Finnish (FIN) AF: 0.265 AC: 2785 AN: 10514

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.434 AC: 29464 AN: 67934

Other (OTH) AF: 0.410 AC: 863 AN: 2106

Alfa AF: 0.419 Hom.: 37223

Bravo AF: 0.392

Asia WGS AF: 0.318 AC: 1106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.5
DANN	Benign	0.59
PhyloP100		0.029

Splicing

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

Other links and lift over

dbSNP: rs10465850; hg19: chr1-65699203;