15-70642823-T-G

Position:

• chr15-70642823-T-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC107984791 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984791	XR_001751595.2	n.4531A>C		non_coding_transcript_exon_variant	3/3

Ensembl

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

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

Gnomad4 AFR AF: 0.695

Gnomad4 AMR AF: 0.899

Gnomad4 ASJ AF: 0.897

Gnomad4 EAS AF: 0.643

Gnomad4 SAS AF: 0.807

Gnomad4 FIN AF: 0.813

Gnomad4 NFE AF: 0.881

Gnomad4 OTH AF: 0.841

Alfa AF: 0.859 Hom.: 17290

Bravo AF: 0.818

Asia WGS AF: 0.738 AC: 2567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8034258; hg19: chr15-70935162;