chr10-130884466-T-C

Variant names:

• chr10-130884466-T-C
• rs4751295

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 0.756 in 152,116 control chromosomes in the GnomAD database, including 43,796 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 0.76 (43796 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.63
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.86 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: 0.756 AC: 114980 AN: 151998 Hom.: 43789 Cov.: 32

Gnomad AFR AF: 0.660

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.835

Gnomad ASJ AF: 0.806

Gnomad EAS AF: 0.882

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.779

Gnomad OTH AF: 0.765

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

GnomAD4 genome AF: 0.756 AC: 115036 AN: 152116 Hom.: 43796 Cov.: 32 AF XY: 0.758 AC XY: 56364 AN XY: 74366

African (AFR) AF: 0.660 AC: 27376 AN: 41470

American (AMR) AF: 0.836 AC: 12770 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.806 AC: 2797 AN: 3472

East Asian (EAS) AF: 0.881 AC: 4547 AN: 5160

South Asian (SAS) AF: 0.728 AC: 3511 AN: 4822

European-Finnish (FIN) AF: 0.813 AC: 8610 AN: 10588

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.778 AC: 52940 AN: 68006

Other (OTH) AF: 0.762 AC: 1609 AN: 2112

Alfa AF: 0.773 Hom.: 191370

Bravo AF: 0.754

Asia WGS AF: 0.798 AC: 2778 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	0.035
DANN	Benign	0.42
PhyloP100		-3.6

Splicing

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

Other links and lift over

dbSNP: rs4751295; hg19: chr10-132682729;