5-151166504-G-A

Variant names:

• chr5-151166504-G-A
• rs13155012
• ENST00000757028.1:n.118-1797C>T

Variant summary

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

The ENST00000757028.1(ENSG00000298634):​n.118-1797C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0573 in 150,148 control chromosomes in the GnomAD database, including 260 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 0.057 (260 hom., cov: 31)
• Consequence: ENSG00000298634 ENST00000757028.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.613
• Publications: 1 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0641 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000757028.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298634	ENST00000757028.1		n.118-1797C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0573 AC: 8604 AN: 150034 Hom.: 260 Cov.: 31

Gnomad AFR AF: 0.0534

Gnomad AMI AF: 0.0123

Gnomad AMR AF: 0.0654

Gnomad ASJ AF: 0.0370

Gnomad EAS AF: 0.00386

Gnomad SAS AF: 0.0514

Gnomad FIN AF: 0.0495

Gnomad MID AF: 0.00955

Gnomad NFE AF: 0.0658

Gnomad OTH AF: 0.0506

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

GnomAD4 genome AF: 0.0573 AC: 8608 AN: 150148 Hom.: 260 Cov.: 31 AF XY: 0.0569 AC XY: 4172 AN XY: 73282

African (AFR) AF: 0.0534 AC: 2203 AN: 41270

American (AMR) AF: 0.0655 AC: 990 AN: 15120

Ashkenazi Jewish (ASJ) AF: 0.0370 AC: 127 AN: 3432

East Asian (EAS) AF: 0.00368 AC: 19 AN: 5168

South Asian (SAS) AF: 0.0514 AC: 238 AN: 4628

European-Finnish (FIN) AF: 0.0495 AC: 510 AN: 10294

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0657 AC: 4403 AN: 66990

Other (OTH) AF: 0.0501 AC: 103 AN: 2056

Alfa AF: 0.0593 Hom.: 51

Bravo AF: 0.0565

Asia WGS AF: 0.0190 AC: 69 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.66
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs13155012; hg19: chr5-150546065;