5-136385759-C-G

Variant names:

• chr5-136385759-C-G
• rs2673913
• ENST00000514282.2:n.174-9153G>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000514282.2(ENSG00000279240):​n.174-9153G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.623 in 152,052 control chromosomes in the GnomAD database, including 30,453 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 0.62 (30453 hom., cov: 32)
• Consequence: ENSG00000279240 ENST00000514282.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.49
• Publications: 4 publications found

Genes affected

ENSG00000279240 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.773 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000514282.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000279240	ENST00000514282.2	TSL:3	n.174-9153G>C		intron	N/A
	ENSG00000279240	ENST00000800861.1		n.201-9153G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.623 AC: 94680 AN: 151934 Hom.: 30448 Cov.: 32

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.794

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.623 AC: 94708 AN: 152052 Hom.: 30453 Cov.: 32 AF XY: 0.629 AC XY: 46750 AN XY: 74316

African (AFR) AF: 0.449 AC: 18604 AN: 41448

American (AMR) AF: 0.687 AC: 10489 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.620 AC: 2151 AN: 3470

East Asian (EAS) AF: 0.582 AC: 3011 AN: 5170

South Asian (SAS) AF: 0.794 AC: 3831 AN: 4822

European-Finnish (FIN) AF: 0.697 AC: 7381 AN: 10584

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.694 AC: 47181 AN: 67970

Other (OTH) AF: 0.630 AC: 1329 AN: 2110

Alfa AF: 0.551 Hom.: 1726

Bravo AF: 0.605

Asia WGS AF: 0.661 AC: 2297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	16
DANN	Benign	0.72
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs2673913; hg19: chr5-135721447;