15-36473855-T-C

Variant names:

• chr15-36473855-T-C
• rs17703807
• ENST00000743889.1:n.377-16359T>C

Variant summary

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

The ENST00000743889.1(ENSG00000296959):​n.377-16359T>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: ENSG00000296959 ENST00000743889.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.200
• Publications: 3 publications found

Genes affected

ENSG00000296959 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000296959	ENST00000743889.1	n.377-16359T>C		intron_variant	Intron 2 of 3
ENSG00000296959	ENST00000743890.1	n.239-16359T>C		intron_variant	Intron 2 of 3
ENSG00000296959	ENST00000743891.1	n.253-16359T>C		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.234 AC: 9715 AN: 41506

American (AMR) AF: 0.225 AC: 3434 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1170 AN: 3468

East Asian (EAS) AF: 0.297 AC: 1538 AN: 5170

South Asian (SAS) AF: 0.243 AC: 1174 AN: 4824

European-Finnish (FIN) AF: 0.289 AC: 3054 AN: 10578

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20627 AN: 67980

Other (OTH) AF: 0.277 AC: 585 AN: 2112

Alfa AF: 0.293 Hom.: 5525

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
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs17703807; hg19: chr15-36766056;