15-70642823-T-G

Variant names:

• chr15-70642823-T-G
• rs8034258
• XR_001751595.2:n.4531A>C

Variant summary

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

The XR_001751595.2(LOC107984791):​n.4531A>C 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 0.817 in 152,222 control chromosomes in the GnomAD database, including 51,407 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 0.82 (51407 hom., cov: 33)
• Consequence: LOC107984791 XR_001751595.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780
• Publications: 2 publications found

Genes affected

LOC107984791 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.887 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: 0.817 AC: 124256 AN: 152104 Hom.: 51384 Cov.: 33

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.849

Gnomad AMR AF: 0.899

Gnomad ASJ AF: 0.897

Gnomad EAS AF: 0.643

Gnomad SAS AF: 0.807

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.881

Gnomad OTH AF: 0.847

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

GnomAD4 genome AF: 0.817 AC: 124327 AN: 152222 Hom.: 51407 Cov.: 33 AF XY: 0.815 AC XY: 60633 AN XY: 74432

African (AFR) AF: 0.695 AC: 28863 AN: 41506

American (AMR) AF: 0.899 AC: 13761 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.897 AC: 3113 AN: 3470

East Asian (EAS) AF: 0.643 AC: 3332 AN: 5178

South Asian (SAS) AF: 0.807 AC: 3901 AN: 4832

European-Finnish (FIN) AF: 0.813 AC: 8616 AN: 10600

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.881 AC: 59926 AN: 68016

Other (OTH) AF: 0.841 AC: 1777 AN: 2114

Alfa AF: 0.858 Hom.: 21807

Bravo AF: 0.818

Asia WGS AF: 0.738 AC: 2567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.7
DANN	Benign	0.50
PhyloP100		-0.078

Splicing

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

Other links and lift over

dbSNP: rs8034258; hg19: chr15-70935162;