rs17288584

Variant names:

• chr18-71467426-G-A
• rs17288584
• ENST00000756734.1:n.96+35278G>A

Your query was ambiguous. Multiple possible variants found:

• chr18-71467426-G-A
• chr18-71467426-G-C

Variant summary

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

The ENST00000756734.1(ENSG00000298599):​n.96+35278G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.036 in 152,184 control chromosomes in the GnomAD database, including 157 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 0.036 (157 hom., cov: 32)
• Consequence: ENSG00000298599 ENST00000756734.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.268
• Publications: 1 publications found

Genes affected

ENSG00000298599 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985179	XR_001753502.1	n.64+35278G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298599	ENST00000756734.1	n.96+35278G>A		intron_variant	Intron 1 of 4
ENSG00000298599	ENST00000756735.1	n.52+35278G>A		intron_variant	Intron 1 of 2
ENSG00000298599	ENST00000756736.1	n.134+35278G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0360 AC: 5478 AN: 152068 Hom.: 157 Cov.: 32

Gnomad AFR AF: 0.00845

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0195

Gnomad ASJ AF: 0.0228

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0275

Gnomad FIN AF: 0.0608

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0573

Gnomad OTH AF: 0.0272

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

GnomAD4 genome AF: 0.0360 AC: 5475 AN: 152184 Hom.: 157 Cov.: 32 AF XY: 0.0350 AC XY: 2604 AN XY: 74390

African (AFR) AF: 0.00843 AC: 350 AN: 41524

American (AMR) AF: 0.0194 AC: 297 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0228 AC: 79 AN: 3468

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5182

South Asian (SAS) AF: 0.0274 AC: 132 AN: 4822

European-Finnish (FIN) AF: 0.0608 AC: 643 AN: 10580

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0573 AC: 3897 AN: 68014

Other (OTH) AF: 0.0269 AC: 57 AN: 2116

Alfa AF: 0.0483 Hom.: 354

Bravo AF: 0.0318

Asia WGS AF: 0.0110 AC: 37 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.25
DANN	Benign	0.60
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs17288584; hg19: chr18-69134662;