5-24226783-C-G

Position:

• chr5-24226783-C-G

Variant summary

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

The ENST00000652008.2(ENSG00000286134):​n.254+44785G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.716 in 152,018 control chromosomes in the GnomAD database, including 39,175 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 0.72 (39175 hom., cov: 31)
• Consequence: ENSG00000286134 ENST00000652008.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00

Genes affected

ENSG00000286134 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000286134	ENST00000652008.2	n.254+44785G>C		intron_variant
ENSG00000286134	ENST00000657726.1	n.283-18475G>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.716 AC: 108707 AN: 151900 Hom.: 39128 Cov.: 31

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.705

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.895

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.732

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

GnomAD4 genome AF: 0.716 AC: 108809 AN: 152018 Hom.: 39175 Cov.: 31 AF XY: 0.715 AC XY: 53099 AN XY: 74284

Gnomad4 AFR AF: 0.672

Gnomad4 AMR AF: 0.719

Gnomad4 ASJ AF: 0.895

Gnomad4 EAS AF: 0.591

Gnomad4 SAS AF: 0.725

Gnomad4 FIN AF: 0.696

Gnomad4 NFE AF: 0.743

Gnomad4 OTH AF: 0.735

Alfa AF: 0.653 Hom.: 2123

Bravo AF: 0.717

Asia WGS AF: 0.679 AC: 2364 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	0.80
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4443391; hg19: chr5-24226892;