chr10-49331978-T-C

Position:

• chr10-49331978-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 0.829 in 152,162 control chromosomes in the GnomAD database, including 52,438 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 0.83 (52438 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.846 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: 0.830 AC: 126125 AN: 152042 Hom.: 52422 Cov.: 31

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.858

Gnomad ASJ AF: 0.807

Gnomad EAS AF: 0.800

Gnomad SAS AF: 0.726

Gnomad FIN AF: 0.826

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.830

Gnomad OTH AF: 0.816

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

GnomAD4 genome AF: 0.829 AC: 126192 AN: 152162 Hom.: 52438 Cov.: 31 AF XY: 0.828 AC XY: 61602 AN XY: 74394

Gnomad4 AFR AF: 0.838

Gnomad4 AMR AF: 0.858

Gnomad4 ASJ AF: 0.807

Gnomad4 EAS AF: 0.800

Gnomad4 SAS AF: 0.725

Gnomad4 FIN AF: 0.826

Gnomad4 NFE AF: 0.830

Gnomad4 OTH AF: 0.813

Alfa AF: 0.826 Hom.: 87016

Bravo AF: 0.833

Asia WGS AF: 0.757 AC: 2631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10745259; hg19: chr10-50540023;