rs869538

Positions:

• chr4-153034646-C-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, non coding transcript 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: ENST00000515232.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.225

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000515232.1	n.49+387C>T		intron_variant, non_coding_transcript_variant		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;