10-80746057-C-T

Variant names:

• chr10-80746057-C-T
• rs2344769

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;