rs1459062

chr4-119128503-G-A

Variant summary

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

The XR_007058251.1(LOC105377395):n.100C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 151,874 control chromosomes in the GnomAD database, including 16,801 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 0.47 (16801 hom., cov: 32)
• Consequence: LOC105377395 XR_007058251.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140

Genes affected

LOC105377395 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377395	XR_007058251.1	n.100C>T		non_coding_transcript_exon_variant	1/5
LOC102723967	XR_001741422.1	n.194-4309G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70738 AN: 151756 Hom.: 16802 Cov.: 32

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.466 AC: 70757 AN: 151874 Hom.: 16801 Cov.: 32 AF XY: 0.465 AC XY: 34525 AN XY: 74198

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.631

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.475

Gnomad4 NFE AF: 0.492

Gnomad4 OTH AF: 0.460

Alfa AF: 0.462 Hom.: 2817

Bravo AF: 0.466

Asia WGS AF: 0.478 AC: 1663 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	4.7
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1459062; hg19: chr4-120049658;