10-80034407-T-C

Position:

• chr10-80034407-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 0.608 in 150,550 control chromosomes in the GnomAD database, including 28,324 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 0.61 (28324 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.930

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.715 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: 0.608 AC: 91417 AN: 150442 Hom.: 28271 Cov.: 28

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.598

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

GnomAD4 genome AF: 0.608 AC: 91525 AN: 150550 Hom.: 28324 Cov.: 28 AF XY: 0.608 AC XY: 44550 AN XY: 73316

Gnomad4 AFR AF: 0.700

Gnomad4 AMR AF: 0.557

Gnomad4 ASJ AF: 0.548

Gnomad4 EAS AF: 0.533

Gnomad4 SAS AF: 0.735

Gnomad4 FIN AF: 0.560

Gnomad4 NFE AF: 0.570

Gnomad4 OTH AF: 0.601

Alfa AF: 0.570 Hom.: 29540

Bravo AF: 0.607

Asia WGS AF: 0.650 AC: 2260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.4
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2342606; hg19: chr10-81794163;