ENST00000651370.1:n.185+4646G>T

Variant names:

• chr1-234927823-C-A
• rs12133603
• ENST00000651370.1:n.185+4646G>T

Variant summary

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

The ENST00000651370.1(ENSG00000286263):​n.185+4646G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,114 control chromosomes in the GnomAD database, including 1,489 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 0.13 (1489 hom., cov: 31)
• Consequence: ENSG00000286263 ENST00000651370.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317

Genes affected

ENSG00000286263 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.154 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
ENSG00000286263	ENST00000651370.1	n.185+4646G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19803 AN: 151996 Hom.: 1490 Cov.: 31

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.0850

Gnomad ASJ AF: 0.0757

Gnomad EAS AF: 0.000961

Gnomad SAS AF: 0.0711

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.130 AC: 19807 AN: 152114 Hom.: 1489 Cov.: 31 AF XY: 0.132 AC XY: 9826 AN XY: 74390

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.0847

Gnomad4 ASJ AF: 0.0757

Gnomad4 EAS AF: 0.000963

Gnomad4 SAS AF: 0.0712

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.112

Alfa AF: 0.156 Hom.: 327

Bravo AF: 0.114

Asia WGS AF: 0.0390 AC: 137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.5
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12133603; hg19: chr1-235063570;