7-136753631-C-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000234352 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000234352	ENST00000586239.5	n.466+32068G>C		intron_variant	Intron 3 of 4	5
ENSG00000234352	ENST00000593789.5	n.335-9643G>C		intron_variant	Intron 3 of 3	5
ENSG00000234352	ENST00000597642.5	n.276-1141G>C		intron_variant	Intron 2 of 3	5
ENSG00000234352	ENST00000598184.1	n.349-1141G>C		intron_variant	Intron 2 of 2	5

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

Gnomad4 AFR AF: 0.629

Gnomad4 AMR AF: 0.898

Gnomad4 ASJ AF: 0.901

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.938

Gnomad4 FIN AF: 0.864

Gnomad4 NFE AF: 0.880

Gnomad4 OTH AF: 0.844

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1593218; hg19: chr7-136438378;