18-71581359-T-C

Variant names:

• chr18-71581359-T-C
• rs1539909
• ENST00000756734.1:n.181+33304T>C

Variant summary

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

The ENST00000756734.1(ENSG00000298599):​n.181+33304T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.862 in 152,102 control chromosomes in the GnomAD database, including 56,670 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 0.86 (56670 hom., cov: 32)
• Consequence: ENSG00000298599 ENST00000756734.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 6 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 (SAS) allele frequency at 95% confidence interval = 0.907 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000756734.1. 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
	ENSG00000298599	ENST00000756734.1		n.181+33304T>C		intron	N/A
	ENSG00000298599	ENST00000756735.1		n.137+33304T>C		intron	N/A
	ENSG00000298599	ENST00000756736.1		n.220-12865T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.862 AC: 131055 AN: 151984 Hom.: 56664 Cov.: 32

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.771

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.926

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.931

Gnomad FIN AF: 0.860

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.894

Gnomad OTH AF: 0.874

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

GnomAD4 genome AF: 0.862 AC: 131109 AN: 152102 Hom.: 56670 Cov.: 32 AF XY: 0.861 AC XY: 64037 AN XY: 74342

African (AFR) AF: 0.797 AC: 33091 AN: 41494

American (AMR) AF: 0.852 AC: 13007 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.926 AC: 3215 AN: 3472

East Asian (EAS) AF: 0.898 AC: 4638 AN: 5164

South Asian (SAS) AF: 0.930 AC: 4485 AN: 4822

European-Finnish (FIN) AF: 0.860 AC: 9100 AN: 10580

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.894 AC: 60760 AN: 67992

Other (OTH) AF: 0.868 AC: 1836 AN: 2114

Alfa AF: 0.887 Hom.: 260111

Bravo AF: 0.857

Asia WGS AF: 0.901 AC: 3134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.23
DANN	Benign	0.58
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1539909; hg19: chr18-69248595;