chr5-151167583-C-T

Variant names:

• chr5-151167583-C-T
• rs366307
• ENST00000757028.1:n.117+1429G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000757028.1(ENSG00000298634):​n.117+1429G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 151,924 control chromosomes in the GnomAD database, including 19,478 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 0.50 (19478 hom., cov: 31)
• Consequence: ENSG00000298634 ENST00000757028.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.751
• Publications: 2 publications found

Genes affected

ENSG00000298634 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.625 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
ENSG00000298634	ENST00000757028.1	n.117+1429G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.499 AC: 75744 AN: 151806 Hom.: 19468 Cov.: 31

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.499 AC: 75790 AN: 151924 Hom.: 19478 Cov.: 31 AF XY: 0.493 AC XY: 36615 AN XY: 74238

African (AFR) AF: 0.631 AC: 26150 AN: 41410

American (AMR) AF: 0.454 AC: 6934 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 1676 AN: 3468

East Asian (EAS) AF: 0.291 AC: 1506 AN: 5168

South Asian (SAS) AF: 0.291 AC: 1400 AN: 4818

European-Finnish (FIN) AF: 0.456 AC: 4812 AN: 10548

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.467 AC: 31701 AN: 67932

Other (OTH) AF: 0.488 AC: 1030 AN: 2110

Alfa AF: 0.485 Hom.: 3662

Bravo AF: 0.509

Asia WGS AF: 0.327 AC: 1134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.70
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs366307; hg19: chr5-150547144;