4-53877079-A-G

Position:

• chr4-53877079-A-G

Variant summary

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

The ENST00000507166.5(ENSG00000282278):​c.1018-397846A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.69 in 152,030 control chromosomes in the GnomAD database, including 38,674 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 0.69 (38674 hom., cov: 33)
• Consequence: ENSG00000282278 ENST00000507166.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108

Genes affected

ENSG00000282278 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.936 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.53877079A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000282278	ENST00000507166.5	c.1018-397846A>G		intron_variant		2		ENSP00000423325.1

Frequencies

GnomAD3 genomes AF: 0.691 AC: 104902 AN: 151912 Hom.: 38654 Cov.: 33

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.958

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.748

Gnomad NFE AF: 0.778

Gnomad OTH AF: 0.711

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

GnomAD4 genome AF: 0.690 AC: 104965 AN: 152030 Hom.: 38674 Cov.: 33 AF XY: 0.699 AC XY: 51958 AN XY: 74346

Gnomad4 AFR AF: 0.411

Gnomad4 AMR AF: 0.791

Gnomad4 ASJ AF: 0.719

Gnomad4 EAS AF: 0.958

Gnomad4 SAS AF: 0.840

Gnomad4 FIN AF: 0.866

Gnomad4 NFE AF: 0.778

Gnomad4 OTH AF: 0.714

Alfa AF: 0.733 Hom.: 5346

Bravo AF: 0.674

Asia WGS AF: 0.878 AC: 3051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.4
DANN	Benign	0.48

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2102010; hg19: chr4-54743246;