chr4-144600715-A-G

Variant names:

• chr4-144600715-A-G
• rs2035901
• ENST00000649263.1:n.328-184737T>C

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285713	ENST00000649263.1	n.328-184737T>C		intron_variant	Intron 4 of 8			ENSP00000497507.1
ENSG00000285783	ENST00000650526.1	n.222+154442T>C		intron_variant	Intron 2 of 14

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;