15-47878180-C-G

Variant names:

• chr15-47878180-C-G
• rs504376
• ENST00000662551.1:n.188+65264C>G

Variant summary

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

The ENST00000662551.1(ENSG00000259754):​n.188+65264C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.55 in 152,018 control chromosomes in the GnomAD database, including 28,348 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 0.55 (28348 hom., cov: 32)
• Consequence: ENSG00000259754 ENST00000662551.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.252
• Publications: 0 publications found

Genes affected

ENSG00000259754 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259754	ENST00000662551.1	n.188+65264C>G		intron_variant	Intron 1 of 2
ENSG00000259754	ENST00000664705.1	n.188+65264C>G		intron_variant	Intron 1 of 5
ENSG00000259754	ENST00000665188.1	n.68+65264C>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.550 AC: 83612 AN: 151900 Hom.: 28351 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.687

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.550 AC: 83611 AN: 152018 Hom.: 28348 Cov.: 32 AF XY: 0.548 AC XY: 40731 AN XY: 74294

African (AFR) AF: 0.158 AC: 6571 AN: 41464

American (AMR) AF: 0.595 AC: 9093 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.704 AC: 2439 AN: 3466

East Asian (EAS) AF: 0.273 AC: 1412 AN: 5166

South Asian (SAS) AF: 0.532 AC: 2560 AN: 4810

European-Finnish (FIN) AF: 0.749 AC: 7911 AN: 10560

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.759 AC: 51585 AN: 67966

Other (OTH) AF: 0.583 AC: 1231 AN: 2112

Alfa AF: 0.569 Hom.: 2375

Bravo AF: 0.520

Asia WGS AF: 0.363 AC: 1266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	11
DANN	Benign	0.61
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs504376; hg19: chr15-48170377;