15-37383382-C-T

Variant names:

• chr15-37383382-C-T
• rs603165
• ENST00000561054.2:n.314-16280G>A

Variant summary

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

The ENST00000561054.2(ENSG00000259434):​n.314-16280G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.541 in 151,240 control chromosomes in the GnomAD database, including 23,127 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 0.54 (23127 hom., cov: 28)
• Consequence: ENSG00000259434 ENST00000561054.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69
• Publications: 4 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370772	XR_932115.3	n.221-16280G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259434	ENST00000561054.2	n.314-16280G>A		intron_variant	Intron 3 of 4	3
ENSG00000259434	ENST00000663330.1	n.242-16280G>A		intron_variant	Intron 2 of 3
ENSG00000259434	ENST00000669587.1	n.388-16280G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.541 AC: 81753 AN: 151122 Hom.: 23105 Cov.: 28

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.541 AC: 81825 AN: 151240 Hom.: 23127 Cov.: 28 AF XY: 0.541 AC XY: 39983 AN XY: 73858

African (AFR) AF: 0.720 AC: 29678 AN: 41212

American (AMR) AF: 0.462 AC: 6992 AN: 15132

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1291 AN: 3460

East Asian (EAS) AF: 0.604 AC: 3072 AN: 5086

South Asian (SAS) AF: 0.360 AC: 1729 AN: 4806

European-Finnish (FIN) AF: 0.564 AC: 5902 AN: 10464

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.467 AC: 31663 AN: 67782

Other (OTH) AF: 0.500 AC: 1048 AN: 2096

Alfa AF: 0.494 Hom.: 17963

Bravo AF: 0.544

Asia WGS AF: 0.484 AC: 1686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.62
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs603165; hg19: chr15-37675583;