4-144765995-C-T

Variant names:

• chr4-144765995-C-T
• rs4835186
• ENST00000649263.1:n.327+298577G>A

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.327+298577G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 151,850 control chromosomes in the GnomAD database, including 2,364 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 0.15 (2364 hom., cov: 32)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.313

Genes affected

ENSG00000285713 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.285 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.327+298577G>A		intron_variant	Intron 4 of 8			ENSP00000497507.1
ENSG00000285783	ENST00000650526.1	n.94-10710G>A		intron_variant	Intron 1 of 14

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22384 AN: 151732 Hom.: 2349 Cov.: 32

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.0871

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0633

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.148 AC: 22447 AN: 151850 Hom.: 2364 Cov.: 32 AF XY: 0.153 AC XY: 11349 AN XY: 74224

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.111

Gnomad4 EAS AF: 0.298

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.0871

Gnomad4 NFE AF: 0.0633

Gnomad4 OTH AF: 0.128

Alfa AF: 0.0817 Hom.: 1253

Bravo AF: 0.157

Asia WGS AF: 0.264 AC: 916 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.6
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4835186; hg19: chr4-145687147;