15-78406417-C-T

Position:

• chr15-78406417-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC105370912 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105370912	XR_932506.3	n.68C>T		non_coding_transcript_exon_variant	1/4

Ensembl

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

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

Gnomad4 AFR AF: 0.720

Gnomad4 AMR AF: 0.640

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.513

Gnomad4 SAS AF: 0.650

Gnomad4 FIN AF: 0.622

Gnomad4 NFE AF: 0.573

Gnomad4 OTH AF: 0.627

Alfa AF: 0.573 Hom.: 22141

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7163013; hg19: chr15-78698759;