ENST00000515232.1:n.49+387C>T

Variant names:

• chr4-153034646-C-T
• rs869538
• ENST00000515232.1:n.49+387C>T

Variant summary

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

The ENST00000515232.1(ENSG00000249022):​n.49+387C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 151,978 control chromosomes in the GnomAD database, including 7,659 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 0.31 (7659 hom., cov: 32)
• Consequence: ENSG00000249022 ENST00000515232.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.225

Genes affected

ENSG00000249022 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.427 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
ENSG00000249022	ENST00000515232.1	n.49+387C>T		intron_variant	Intron 1 of 4	4

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46395 AN: 151858 Hom.: 7650 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.306 AC: 46449 AN: 151978 Hom.: 7659 Cov.: 32 AF XY: 0.304 AC XY: 22576 AN XY: 74276

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.436

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.340

Gnomad4 OTH AF: 0.344

Alfa AF: 0.315 Hom.: 990

Bravo AF: 0.321

Asia WGS AF: 0.324 AC: 1126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.7
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs869538; hg19: chr4-153955798;