10-80746057-C-T

Position:

• chr10-80746057-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 0.416 in 152,014 control chromosomes in the GnomAD database, including 16,134 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 0.42 (16134 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206

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 (NFE) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63310 AN: 151896 Hom.: 16135 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.416 AC: 63302 AN: 152014 Hom.: 16134 Cov.: 32 AF XY: 0.411 AC XY: 30560 AN XY: 74308

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.626

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.321

Gnomad4 FIN AF: 0.545

Gnomad4 NFE AF: 0.579

Gnomad4 OTH AF: 0.460

Alfa AF: 0.521 Hom.: 9900

Bravo AF: 0.393

Asia WGS AF: 0.277 AC: 968 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	3.0
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2344769; hg19: chr10-82505813;