10-80322584-T-C

Position:

• chr10-80322584-T-C

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 0.0631 in 152,282 control chromosomes in the GnomAD database, including 378 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 (378 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0772 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: 0.0632 AC: 9612 AN: 152162 Hom.: 377 Cov.: 32

Gnomad AFR AF: 0.0796

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0605

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.000576

Gnomad SAS AF: 0.0416

Gnomad FIN AF: 0.0612

Gnomad MID AF: 0.0892

Gnomad NFE AF: 0.0576

Gnomad OTH AF: 0.0679

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

GnomAD4 genome AF: 0.0631 AC: 9614 AN: 152282 Hom.: 378 Cov.: 32 AF XY: 0.0627 AC XY: 4670 AN XY: 74464

Gnomad4 AFR AF: 0.0795

Gnomad4 AMR AF: 0.0603

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0425

Gnomad4 FIN AF: 0.0612

Gnomad4 NFE AF: 0.0575

Gnomad4 OTH AF: 0.0667

Alfa AF: 0.0596 Hom.: 256

Bravo AF: 0.0620

Asia WGS AF: 0.0240 AC: 84 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.8
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2066167; hg19: chr10-82082340;