rs10509739

Positions:

• chr10-99873553-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 0.063 in 152,178 control chromosomes in the GnomAD database, including 437 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 0.063 (437 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.795

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.102 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: 0.0630 AC: 9581 AN: 152060 Hom.: 436 Cov.: 32

Gnomad AFR AF: 0.0143

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0790

Gnomad EAS AF: 0.000772

Gnomad SAS AF: 0.0334

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0808

Gnomad OTH AF: 0.0569

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

GnomAD4 genome AF: 0.0630 AC: 9588 AN: 152178 Hom.: 437 Cov.: 32 AF XY: 0.0643 AC XY: 4788 AN XY: 74408

Gnomad4 AFR AF: 0.0143

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.0790

Gnomad4 EAS AF: 0.000774

Gnomad4 SAS AF: 0.0330

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.0808

Gnomad4 OTH AF: 0.0559

Alfa AF: 0.0765 Hom.: 285

Bravo AF: 0.0618

Asia WGS AF: 0.0220 AC: 78 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.76
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10509739; hg19: chr10-101633310;