15-36473855-T-C

Variant names:

• chr15-36473855-T-C
• rs17703807
• XR_932110.1:n.249-11063T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_932110.1(LOC105370768):​n.249-11063T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 152,118 control chromosomes in the GnomAD database, including 5,849 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 0.27 (5849 hom., cov: 33)
• Consequence: LOC105370768 XR_932110.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.200

Genes affected

LOC105370768 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370768	XR_932110.1	n.249-11063T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41735 AN: 152000 Hom.: 5849 Cov.: 33

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.274 AC: 41742 AN: 152118 Hom.: 5849 Cov.: 33 AF XY: 0.274 AC XY: 20347 AN XY: 74366

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.289

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.277

Alfa AF: 0.294 Hom.: 4116

Bravo AF: 0.268

Asia WGS AF: 0.249 AC: 872 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.2
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17703807; hg19: chr15-36766056;