10-84015577-C-T

Variant names:

• chr10-84015577-C-T
• rs10509486

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 0.0717 in 152,210 control chromosomes in the GnomAD database, including 511 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 0.072 (511 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0450

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.145 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: 0.0716 AC: 10889 AN: 152092 Hom.: 508 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0526

Gnomad ASJ AF: 0.0544

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.0519

Gnomad FIN AF: 0.0295

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0487

Gnomad OTH AF: 0.0645

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

GnomAD4 genome AF: 0.0717 AC: 10907 AN: 152210 Hom.: 511 Cov.: 32 AF XY: 0.0698 AC XY: 5194 AN XY: 74418

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.0526

Gnomad4 ASJ AF: 0.0544

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.0513

Gnomad4 FIN AF: 0.0295

Gnomad4 NFE AF: 0.0487

Gnomad4 OTH AF: 0.0643

Alfa AF: 0.0576 Hom.: 49

Bravo AF: 0.0774

Asia WGS AF: 0.109 AC: 379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.8
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10509486; hg19: chr10-85775333;