rs1459062

Variant names:

• chr4-119128503-G-A
• rs1459062
• XR_007058249.1:n.100C>T

Variant summary

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

The XR_007058249.1(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_007058249.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140
• Publications: 4 publications found

Genes affected

LOC105377395 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105377395	XR_007058249.1	n.100C>T		non_coding_transcript_exon_variant	Exon 1 of 4
LOC105377395	XR_007058250.1	n.100C>T		non_coding_transcript_exon_variant	Exon 1 of 4
LOC105377395	XR_007058251.1	n.100C>T		non_coding_transcript_exon_variant	Exon 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307688	ENST00000827905.1	n.-203C>T		upstream_gene_variant

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

African (AFR) AF: 0.403 AC: 16666 AN: 41398

American (AMR) AF: 0.497 AC: 7587 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1459 AN: 3466

East Asian (EAS) AF: 0.631 AC: 3255 AN: 5158

South Asian (SAS) AF: 0.422 AC: 2033 AN: 4812

European-Finnish (FIN) AF: 0.475 AC: 4990 AN: 10506

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.492 AC: 33432 AN: 67946

Other (OTH) AF: 0.460 AC: 972 AN: 2114

Alfa AF: 0.460 Hom.: 2879

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
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs1459062; hg19: chr4-120049658;