3-30305713-T-C

Variant names:

• chr3-30305713-T-C
• rs1495581
• XR_007095854.1:n.*138T>C

Variant summary

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

The XR_007095854.1(LOC124909358):​n.*138T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.748 in 151,874 control chromosomes in the GnomAD database, including 43,094 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 0.75 (43094 hom., cov: 31)
• Consequence: LOC124909358 XR_007095854.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237
• Publications: 4 publications found

Genes affected

LOC124909358 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.862 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124909358	XR_007095854.1	n.*138T>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.748 AC: 113448 AN: 151756 Hom.: 43044 Cov.: 31

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.748 AC: 113561 AN: 151874 Hom.: 43094 Cov.: 31 AF XY: 0.751 AC XY: 55755 AN XY: 74218

African (AFR) AF: 0.870 AC: 36037 AN: 41434

American (AMR) AF: 0.757 AC: 11551 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2176 AN: 3468

East Asian (EAS) AF: 0.826 AC: 4248 AN: 5144

South Asian (SAS) AF: 0.824 AC: 3959 AN: 4806

European-Finnish (FIN) AF: 0.699 AC: 7350 AN: 10518

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.675 AC: 45871 AN: 67930

Other (OTH) AF: 0.704 AC: 1488 AN: 2114

Alfa AF: 0.703 Hom.: 20534

Bravo AF: 0.752

Asia WGS AF: 0.816 AC: 2837 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.64
DANN	Benign	0.63
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs1495581; hg19: chr3-30347204;