10-30201775-C-T

Variant names:

• chr10-30201775-C-T
• rs2462021
• XR_930791.2:n.1449-1712C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_930791.2(LOC105376477):​n.1449-1712C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 152,104 control chromosomes in the GnomAD database, including 23,414 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 0.52 (23414 hom., cov: 33)
• Consequence: LOC105376477 XR_930791.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.82
• Publications: 17 publications found

Genes affected

LOC105376477 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78818 AN: 151986 Hom.: 23406 Cov.: 33

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.780

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.518 AC: 78837 AN: 152104 Hom.: 23414 Cov.: 33 AF XY: 0.522 AC XY: 38791 AN XY: 74356

African (AFR) AF: 0.236 AC: 9802 AN: 41480

American (AMR) AF: 0.560 AC: 8566 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.616 AC: 2137 AN: 3470

East Asian (EAS) AF: 0.239 AC: 1241 AN: 5182

South Asian (SAS) AF: 0.517 AC: 2495 AN: 4824

European-Finnish (FIN) AF: 0.741 AC: 7828 AN: 10566

Middle Eastern (MID) AF: 0.538 AC: 155 AN: 288

European-Non Finnish (NFE) AF: 0.659 AC: 44778 AN: 67988

Other (OTH) AF: 0.533 AC: 1125 AN: 2112

Alfa AF: 0.601 Hom.: 112107

Bravo AF: 0.489

Asia WGS AF: 0.372 AC: 1299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.068
DANN	Benign	0.42
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs2462021; hg19: chr10-30490704;