chr10-58301486-A-G

Variant names:

• chr10-58301486-A-G
• rs965867

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 0.236 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
• Publications: 5 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 (AFR) allele frequency at 95% confidence interval = 0.416 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: 0.236 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

African (AFR) AF: 0.421 AC: 17422 AN: 41360

American (AMR) AF: 0.184 AC: 2810 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 506 AN: 3472

East Asian (EAS) AF: 0.311 AC: 1599 AN: 5146

South Asian (SAS) AF: 0.175 AC: 844 AN: 4816

European-Finnish (FIN) AF: 0.158 AC: 1665 AN: 10536

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10449 AN: 67950

Other (OTH) AF: 0.205 AC: 432 AN: 2108

Alfa AF: 0.171 Hom.: 3002

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
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs965867; hg19: chr10-60061246;