rs1451125

chr4-136171235-T-A

Variant summary

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

The ENST00000513332.5(ENSG00000251567):n.280-51097A>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 0.321 in 151,884 control chromosomes in the GnomAD database, including 7,882 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 0.32 (7882 hom., cov: 31)
• Consequence: ENST00000513332.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.44 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
	ENST00000513332.5	n.280-51097A>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48651 AN: 151768 Hom.: 7873 Cov.: 31

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.321 AC: 48683 AN: 151884 Hom.: 7882 Cov.: 31 AF XY: 0.324 AC XY: 24064 AN XY: 74242

Gnomad4 AFR AF: 0.310

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.259

Gnomad4 EAS AF: 0.456

Gnomad4 SAS AF: 0.393

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.308

Gnomad4 OTH AF: 0.318

Alfa AF: 0.319 Hom.: 967

Bravo AF: 0.319

Asia WGS AF: 0.425 AC: 1481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.58
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1451125; hg19: chr4-137092390;