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.

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: 0.748 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 v4.9

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;