15-78406417-C-T

Variant names:

• chr15-78406417-C-T
• rs7163013
• XR_932506.3:n.68C>T

Variant summary

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

The XR_932506.3(LOC105370912):​n.68C>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 0.626 in 151,924 control chromosomes in the GnomAD database, including 30,056 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 0.63 (30056 hom., cov: 31)
• Consequence: LOC105370912 XR_932506.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.11
• Publications: 5 publications found

Genes affected

LOC105370912 (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 = 0.713 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370912	XR_932506.3	n.68C>T		non_coding_transcript_exon_variant	Exon 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299108	ENST00000760515.1	n.230-128C>T		intron_variant	Intron 2 of 2
ENSG00000299108	ENST00000760516.1	n.238-128C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.626 AC: 94955 AN: 151804 Hom.: 30030 Cov.: 31

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.626 AC: 95034 AN: 151924 Hom.: 30056 Cov.: 31 AF XY: 0.628 AC XY: 46594 AN XY: 74240

African (AFR) AF: 0.720 AC: 29856 AN: 41460

American (AMR) AF: 0.640 AC: 9770 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.587 AC: 2037 AN: 3468

East Asian (EAS) AF: 0.513 AC: 2631 AN: 5128

South Asian (SAS) AF: 0.650 AC: 3124 AN: 4804

European-Finnish (FIN) AF: 0.622 AC: 6569 AN: 10560

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.573 AC: 38924 AN: 67918

Other (OTH) AF: 0.627 AC: 1325 AN: 2112

Alfa AF: 0.596 Hom.: 38941

Bravo AF: 0.630

Asia WGS AF: 0.628 AC: 2181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.65
DANN	Benign	0.60
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs7163013; hg19: chr15-78698759;