chr4-144570129-G-A

Variant names:

• chr4-144570129-G-A
• rs1512288
• ENST00000649263.1:n.328-154151C>T

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.328-154151C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 152,036 control chromosomes in the GnomAD database, including 13,284 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 0.41 (13284 hom., cov: 33)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

Genes affected

ENSG00000285713 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.503 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.328-154151C>T		intron_variant	Intron 4 of 8			ENSP00000497507.1
ENSG00000285783	ENST00000650526.1	n.223-154151C>T		intron_variant	Intron 2 of 14

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62916 AN: 151918 Hom.: 13275 Cov.: 33

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.414 AC: 62963 AN: 152036 Hom.: 13284 Cov.: 33 AF XY: 0.419 AC XY: 31137 AN XY: 74298

Gnomad4 AFR AF: 0.407

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.301

Gnomad4 SAS AF: 0.520

Gnomad4 FIN AF: 0.540

Gnomad4 NFE AF: 0.420

Gnomad4 OTH AF: 0.378

Alfa AF: 0.429 Hom.: 7739

Bravo AF: 0.392

Asia WGS AF: 0.385 AC: 1339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1512288; hg19: chr4-145491281;