10-82999183-G-T

Position:

• chr10-82999183-G-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 0.176 in 152,030 control chromosomes in the GnomAD database, including 2,988 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 0.18 (2988 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.247 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: 0.176 AC: 26748 AN: 151912 Hom.: 2986 Cov.: 32

Gnomad AFR AF: 0.0594

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.0293

Gnomad SAS AF: 0.0834

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.176 AC: 26751 AN: 152030 Hom.: 2988 Cov.: 32 AF XY: 0.173 AC XY: 12817 AN XY: 74300

Gnomad4 AFR AF: 0.0594

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.0294

Gnomad4 SAS AF: 0.0853

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.228

Alfa AF: 0.237 Hom.: 5290

Bravo AF: 0.176

Asia WGS AF: 0.0600 AC: 207 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17689242; hg19: chr10-84758939;