ENST00000586239.5:n.466+32068G>C

Variant names:

• chr7-136753631-C-G
• rs1593218
• ENST00000586239.5:n.466+32068G>C

Variant summary

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

The ENST00000586239.5(ENSG00000234352):​n.466+32068G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.818 in 150,512 control chromosomes in the GnomAD database, including 51,398 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 0.82 (51398 hom., cov: 27)
• Consequence: ENSG00000234352 ENST00000586239.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357
• Publications: 1 publications found

Genes affected

ENSG00000234352 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000586239.5. 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
	ENSG00000234352	ENST00000586239.5	TSL:5	n.466+32068G>C		intron	N/A
	ENSG00000234352	ENST00000593789.5	TSL:5	n.335-9643G>C		intron	N/A
	ENSG00000234352	ENST00000597642.5	TSL:5	n.276-1141G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.818 AC: 123078 AN: 150408 Hom.: 51370 Cov.: 27

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.897

Gnomad ASJ AF: 0.901

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.938

Gnomad FIN AF: 0.864

Gnomad MID AF: 0.888

Gnomad NFE AF: 0.880

Gnomad OTH AF: 0.842

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

GnomAD4 genome AF: 0.818 AC: 123155 AN: 150512 Hom.: 51398 Cov.: 27 AF XY: 0.821 AC XY: 60240 AN XY: 73372

African (AFR) AF: 0.629 AC: 25681 AN: 40844

American (AMR) AF: 0.898 AC: 13601 AN: 15154

Ashkenazi Jewish (ASJ) AF: 0.901 AC: 3130 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5104 AN: 5112

South Asian (SAS) AF: 0.938 AC: 4491 AN: 4786

European-Finnish (FIN) AF: 0.864 AC: 8620 AN: 9976

Middle Eastern (MID) AF: 0.885 AC: 255 AN: 288

European-Non Finnish (NFE) AF: 0.880 AC: 59714 AN: 67870

Other (OTH) AF: 0.844 AC: 1775 AN: 2104

Alfa AF: 0.835 Hom.: 6305

Bravo AF: 0.811

Asia WGS AF: 0.956 AC: 3327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.12
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs1593218; hg19: chr7-136438378;