15-87394952-G-A

Position:

• chr15-87394952-G-A

Variant summary

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

The NR_187944.1(LOC102724465):​n.914+11411C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 151,946 control chromosomes in the GnomAD database, including 8,485 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 0.32 (8485 hom., cov: 31)
• Consequence: LOC102724465 NR_187944.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90

Genes affected

ENSG00000259560 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102724465	NR_187944.1	n.914+11411C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000259560	ENST00000656130.1	n.176+38157C>T		intron_variant
ENSG00000259560	ENST00000665121.1	n.332+34946C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49287 AN: 151828 Hom.: 8472 Cov.: 31

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.0333

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.325 AC: 49340 AN: 151946 Hom.: 8485 Cov.: 31 AF XY: 0.318 AC XY: 23592 AN XY: 74244

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.0332

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.384

Gnomad4 OTH AF: 0.348

Alfa AF: 0.346 Hom.: 1832

Bravo AF: 0.321

Asia WGS AF: 0.140 AC: 489 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.9
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11638634; hg19: chr15-87938183;