10-49331978-T-C

Variant names:

• chr10-49331978-T-C
• rs10745259

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 0.829 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.838 AC: 34763 AN: 41496

American (AMR) AF: 0.858 AC: 13117 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.807 AC: 2799 AN: 3470

East Asian (EAS) AF: 0.800 AC: 4132 AN: 5162

South Asian (SAS) AF: 0.725 AC: 3498 AN: 4824

European-Finnish (FIN) AF: 0.826 AC: 8755 AN: 10598

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.830 AC: 56420 AN: 68006

Other (OTH) AF: 0.813 AC: 1718 AN: 2112

Alfa AF: 0.828 Hom.: 141608

Bravo AF: 0.833

Asia WGS AF: 0.757 AC: 2631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.67
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs10745259; hg19: chr10-50540023;