rs1381632

chr4-87647832-T-A

Variant summary

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

The ENST00000506480.5(ENSG00000249001):n.322+25158A>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 0.173 in 152,172 control chromosomes in the GnomAD database, including 2,697 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 0.17 (2697 hom., cov: 32)
• Consequence: ENST00000506480.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.492

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.248 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
	ENST00000506480.5	n.322+25158A>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26364 AN: 152054 Hom.: 2699 Cov.: 32

Gnomad AFR AF: 0.0752

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.173 AC: 26370 AN: 152172 Hom.: 2697 Cov.: 32 AF XY: 0.172 AC XY: 12776 AN XY: 74394

Gnomad4 AFR AF: 0.0752

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.208

Alfa AF: 0.193 Hom.: 379

Bravo AF: 0.178

Asia WGS AF: 0.146 AC: 515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	4.2
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1381632; hg19: chr4-88568984;