10-80746057-C-T

Variant names:

• chr10-80746057-C-T
• rs2344769

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 0.416 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.144 AC: 5972 AN: 41478

American (AMR) AF: 0.364 AC: 5565 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.626 AC: 2171 AN: 3468

East Asian (EAS) AF: 0.225 AC: 1160 AN: 5164

South Asian (SAS) AF: 0.321 AC: 1549 AN: 4824

European-Finnish (FIN) AF: 0.545 AC: 5745 AN: 10536

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.579 AC: 39368 AN: 67960

Other (OTH) AF: 0.460 AC: 968 AN: 2106

Alfa AF: 0.521 Hom.: 11143

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
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs2344769; hg19: chr10-82505813;