rs10509689

Variant names:

• chr10-95585712-G-A
• rs10509689

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 0.137 in 152,178 control chromosomes in the GnomAD database, including 1,566 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 0.14 (1566 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0240

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.184 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: 0.137 AC: 20819 AN: 152060 Hom.: 1565 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.0985

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.137 AC: 20834 AN: 152178 Hom.: 1566 Cov.: 32 AF XY: 0.137 AC XY: 10168 AN XY: 74402

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.278

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.0985

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.173

Alfa AF: 0.149 Hom.: 2538

Bravo AF: 0.135

Asia WGS AF: 0.144 AC: 502 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	9.2
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10509689; hg19: chr10-97345469;