10-59374577-G-A

Variant names:

• chr10-59374577-G-A
• rs10509101

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 0.0976 in 151,998 control chromosomes in the GnomAD database, including 970 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 0.098 (970 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.23 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: 0.0977 AC: 14835 AN: 151878 Hom.: 968 Cov.: 32

Gnomad AFR AF: 0.0337

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0946

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

GnomAD4 genome AF: 0.0976 AC: 14842 AN: 151998 Hom.: 970 Cov.: 32 AF XY: 0.103 AC XY: 7622 AN XY: 74272

African (AFR) AF: 0.0337 AC: 1397 AN: 41492

American (AMR) AF: 0.106 AC: 1612 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 451 AN: 3470

East Asian (EAS) AF: 0.242 AC: 1242 AN: 5142

South Asian (SAS) AF: 0.223 AC: 1066 AN: 4784

European-Finnish (FIN) AF: 0.149 AC: 1571 AN: 10562

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7150 AN: 67982

Other (OTH) AF: 0.0932 AC: 197 AN: 2114

Alfa AF: 0.104 Hom.: 1141

Bravo AF: 0.0894

Asia WGS AF: 0.182 AC: 631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.12
DANN	Benign	0.75
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs10509101; hg19: chr10-61134335;