rs597543

Variant names:

• chr15-47850603-G-A
• rs597543
• ENST00000662551.1:n.188+37687G>A

Variant summary

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

The ENST00000662551.1(ENSG00000259754):​n.188+37687G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.683 in 152,100 control chromosomes in the GnomAD database, including 37,456 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 0.68 (37456 hom., cov: 33)
• Consequence: ENSG00000259754 ENST00000662551.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.233
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.967 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+37687G>A		intron_variant	Intron 1 of 2
ENSG00000259754	ENST00000664705.1	n.188+37687G>A		intron_variant	Intron 1 of 5
ENSG00000259754	ENST00000665188.1	n.68+37687G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.683 AC: 103756 AN: 151982 Hom.: 37385 Cov.: 33

Gnomad AFR AF: 0.888

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.990

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.683 AC: 103894 AN: 152100 Hom.: 37456 Cov.: 33 AF XY: 0.689 AC XY: 51240 AN XY: 74360

African (AFR) AF: 0.888 AC: 36872 AN: 41520

American (AMR) AF: 0.679 AC: 10364 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2015 AN: 3472

East Asian (EAS) AF: 0.990 AC: 5132 AN: 5184

South Asian (SAS) AF: 0.765 AC: 3685 AN: 4816

European-Finnish (FIN) AF: 0.611 AC: 6448 AN: 10552

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.550 AC: 37386 AN: 67972

Other (OTH) AF: 0.636 AC: 1343 AN: 2110

Alfa AF: 0.617 Hom.: 11666

Bravo AF: 0.697

Asia WGS AF: 0.882 AC: 3064 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.5
DANN	Benign	0.37
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs597543; hg19: chr15-48142800;