rs2462021

Positions:

• chr10-30201775-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_930791.2(LOC105376477):​n.1449-1712C>T variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.82

Genes affected

LOC105376477 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376477	XR_930791.2	n.1449-1712C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.560

Gnomad4 ASJ AF: 0.616

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.517

Gnomad4 FIN AF: 0.741

Gnomad4 NFE AF: 0.659

Gnomad4 OTH AF: 0.533

Alfa AF: 0.628 Hom.: 49309

Bravo AF: 0.489

Asia WGS AF: 0.372 AC: 1299 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	0.068
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2462021; hg19: chr10-30490704;