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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000561054.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259434	ENST00000561054.2	TSL:3	n.314-16280G>A		intron	N/A
	ENSG00000259434	ENST00000663330.1		n.242-16280G>A		intron	N/A
	ENSG00000259434	ENST00000669587.1		n.388-16280G>A		intron	N/A

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 v4.9

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;