ENST00000654495.1:n.235+36926C>T

Variant names:

• chr6-68475863-G-A
• rs1565488
• ENST00000654495.1:n.235+36926C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000654495.1(ENSG00000288088):​n.235+36926C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.713 in 151,750 control chromosomes in the GnomAD database, including 39,369 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 0.71 (39369 hom., cov: 30)
• Consequence: ENSG00000288088 ENST00000654495.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

Genes affected

ENSG00000288088 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.822 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
ENSG00000288088	ENST00000654495.1	n.235+36926C>T		intron_variant	Intron 2 of 3
ENSG00000288088	ENST00000657302.1	n.111+100182C>T		intron_variant	Intron 1 of 2
ENSG00000288088	ENST00000669267.1	n.86-8614C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.714 AC: 108191 AN: 151632 Hom.: 39352 Cov.: 30

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.756

Gnomad AMR AF: 0.735

Gnomad ASJ AF: 0.833

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.776

Gnomad OTH AF: 0.745

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

GnomAD4 genome AF: 0.713 AC: 108255 AN: 151750 Hom.: 39369 Cov.: 30 AF XY: 0.715 AC XY: 52999 AN XY: 74162

Gnomad4 AFR AF: 0.557

Gnomad4 AMR AF: 0.735

Gnomad4 ASJ AF: 0.833

Gnomad4 EAS AF: 0.843

Gnomad4 SAS AF: 0.764

Gnomad4 FIN AF: 0.750

Gnomad4 NFE AF: 0.776

Gnomad4 OTH AF: 0.745

Alfa AF: 0.749 Hom.: 15464

Bravo AF: 0.705

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1565488; hg19: chr6-69185755; COSMIC: COSV69403346;