rs17459580

Variant names:

• chr1-159696991-A-C
• rs17459580
• ENST00000751816.1:n.108-29536A>C

Variant summary

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

The ENST00000751816.1(ENSG00000297913):​n.108-29536A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,152 control chromosomes in the GnomAD database, including 1,666 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 0.13 (1666 hom., cov: 32)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.368
• Publications: 1 publications found

Genes affected

ENSG00000297913 (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 (NFE) allele frequency at 95% confidence interval = 0.182 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
ENSG00000297913	ENST00000751816.1	n.108-29536A>C		intron_variant	Intron 1 of 2
ENSG00000297913	ENST00000751817.1	n.110-29536A>C		intron_variant	Intron 1 of 3
ENSG00000297913	ENST00000751818.1	n.63-29536A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19629 AN: 152034 Hom.: 1664 Cov.: 32

Gnomad AFR AF: 0.0349

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.0351

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.129 AC: 19631 AN: 152152 Hom.: 1666 Cov.: 32 AF XY: 0.128 AC XY: 9499 AN XY: 74386

African (AFR) AF: 0.0348 AC: 1448 AN: 41558

American (AMR) AF: 0.128 AC: 1950 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 480 AN: 3470

East Asian (EAS) AF: 0.0349 AC: 181 AN: 5180

South Asian (SAS) AF: 0.128 AC: 616 AN: 4820

European-Finnish (FIN) AF: 0.167 AC: 1768 AN: 10580

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12563 AN: 67964

Other (OTH) AF: 0.132 AC: 278 AN: 2108

Alfa AF: 0.154 Hom.: 260

Bravo AF: 0.121

Asia WGS AF: 0.0660 AC: 231 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	1.3
DANN	Benign	0.46
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs17459580; hg19: chr1-159666781;