4-144600715-A-G

Position:

• chr4-144600715-A-G

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.328-184737T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 151,980 control chromosomes in the GnomAD database, including 28,409 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 0.60 (28409 hom., cov: 31)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.03

Genes affected

ENSG00000285713 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.14).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.144600715A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285713	ENST00000649263.1	n.328-184737T>C		intron_variant				ENSP00000497507.1
ENSG00000285783	ENST00000650526.1	n.222+154442T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.599 AC: 90893 AN: 151862 Hom.: 28374 Cov.: 31

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.763

Gnomad SAS AF: 0.804

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.558

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.562

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

GnomAD4 genome AF: 0.599 AC: 90988 AN: 151980 Hom.: 28409 Cov.: 31 AF XY: 0.606 AC XY: 44981 AN XY: 74280

Gnomad4 AFR AF: 0.751

Gnomad4 AMR AF: 0.584

Gnomad4 ASJ AF: 0.502

Gnomad4 EAS AF: 0.764

Gnomad4 SAS AF: 0.803

Gnomad4 FIN AF: 0.583

Gnomad4 NFE AF: 0.493

Gnomad4 OTH AF: 0.565

Alfa AF: 0.511 Hom.: 10279

Bravo AF: 0.601

Asia WGS AF: 0.802 AC: 2790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.024
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2035901; hg19: chr4-145521867;