15-37338164-T-C

Variant names:

• chr15-37338164-T-C
• rs4924148
• ENST00000756729.1:n.479+28820A>G

Variant summary

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

The ENST00000756729.1(ENSG00000259434):​n.479+28820A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 150,890 control chromosomes in the GnomAD database, including 5,684 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 (5684 hom., cov: 29)
• Consequence: ENSG00000259434 ENST00000756729.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 6 publications found

Genes affected

ENSG00000259434 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.319 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
ENSG00000259434	ENST00000756729.1	n.479+28820A>G		intron_variant	Intron 4 of 4
ENSG00000259434	ENST00000756730.1	n.344+28820A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40024 AN: 150780 Hom.: 5690 Cov.: 29

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.0244

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.265 AC: 40019 AN: 150890 Hom.: 5684 Cov.: 29 AF XY: 0.263 AC XY: 19349 AN XY: 73630

African (AFR) AF: 0.194 AC: 8001 AN: 41140

American (AMR) AF: 0.230 AC: 3489 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1357 AN: 3466

East Asian (EAS) AF: 0.0245 AC: 126 AN: 5146

South Asian (SAS) AF: 0.318 AC: 1519 AN: 4774

European-Finnish (FIN) AF: 0.258 AC: 2626 AN: 10176

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.323 AC: 21852 AN: 67704

Other (OTH) AF: 0.277 AC: 581 AN: 2100

Alfa AF: 0.309 Hom.: 32202

Bravo AF: 0.259

Asia WGS AF: 0.152 AC: 528 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.60
DANN	Benign	0.48
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs4924148; hg19: chr15-37630365;