10-84015577-C-T

Variant names:

• chr10-84015577-C-T
• rs10509486

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 0.0717 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
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• 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

African (AFR) AF: 0.122 AC: 5065 AN: 41490

American (AMR) AF: 0.0526 AC: 804 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0544 AC: 189 AN: 3472

East Asian (EAS) AF: 0.154 AC: 797 AN: 5172

South Asian (SAS) AF: 0.0513 AC: 248 AN: 4832

European-Finnish (FIN) AF: 0.0295 AC: 313 AN: 10610

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0487 AC: 3313 AN: 68020

Other (OTH) AF: 0.0643 AC: 136 AN: 2114

Alfa AF: 0.0600 Hom.: 55

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
PhyloP100		-0.045

Splicing

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

Other links and lift over

dbSNP: rs10509486; hg19: chr10-85775333;