rs965867

chr10-58301486-A-Gchr10-58301486-A-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 0.236 in 151,852 control chromosomes in the GnomAD database, including 5,296 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 0.24 (5296 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35862 AN: 151734 Hom.: 5285 Cov.: 31

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.236 AC: 35906 AN: 151852 Hom.: 5296 Cov.: 31 AF XY: 0.236 AC XY: 17537 AN XY: 74208

Gnomad4 AFR AF: 0.421

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.205

Alfa AF: 0.166 Hom.: 2298

Bravo AF: 0.248

Asia WGS AF: 0.239 AC: 832 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.60
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs965867; hg19: chr10-60061246;