4-137814564-A-G

Variant names:

• chr4-137814564-A-G
• rs1858114
• ENST00000506420.1:n.66-1646A>G

Variant summary

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

The ENST00000506420.1(ENSG00000250034):​n.66-1646A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.899 in 152,160 control chromosomes in the GnomAD database, including 61,496 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 0.90 (61496 hom., cov: 32)
• Consequence: ENSG00000250034 ENST00000506420.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.653

Genes affected

ENSG00000250034 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.934 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
ENSG00000250034	ENST00000506420.1	n.66-1646A>G		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.899 AC: 136610 AN: 152042 Hom.: 61449 Cov.: 32

Gnomad AFR AF: 0.906

Gnomad AMI AF: 0.974

Gnomad AMR AF: 0.937

Gnomad ASJ AF: 0.927

Gnomad EAS AF: 0.956

Gnomad SAS AF: 0.867

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.888

Gnomad OTH AF: 0.907

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

GnomAD4 genome AF: 0.899 AC: 136717 AN: 152160 Hom.: 61496 Cov.: 32 AF XY: 0.898 AC XY: 66747 AN XY: 74364

Gnomad4 AFR AF: 0.906

Gnomad4 AMR AF: 0.937

Gnomad4 ASJ AF: 0.927

Gnomad4 EAS AF: 0.956

Gnomad4 SAS AF: 0.866

Gnomad4 FIN AF: 0.849

Gnomad4 NFE AF: 0.888

Gnomad4 OTH AF: 0.905

Alfa AF: 0.895 Hom.: 7161

Bravo AF: 0.906

Asia WGS AF: 0.895 AC: 3111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1858114; hg19: chr4-138735718;