rs10465850

Positions:

• chr1-65233520-C-T

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 0.387 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.353

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.314

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.410

Alfa AF: 0.426 Hom.: 23102

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10465850; hg19: chr1-65699203;