5-136385759-C-G

Variant names:

• chr5-136385759-C-G
• rs2673913
• ENST00000514282.1:n.156-9153G>C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000514282.1(ENSG00000279240):​n.156-9153G>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 ENST00000514282.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.49

Genes affected

ENSG00000279240 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901075	XR_007058948.1	n.134-9153G>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000279240	ENST00000514282.1	n.156-9153G>C		intron_variant	Intron 1 of 1	3

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

Gnomad4 AFR AF: 0.449

Gnomad4 AMR AF: 0.687

Gnomad4 ASJ AF: 0.620

Gnomad4 EAS AF: 0.582

Gnomad4 SAS AF: 0.794

Gnomad4 FIN AF: 0.697

Gnomad4 NFE AF: 0.694

Gnomad4 OTH AF: 0.630

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2673913; hg19: chr5-135721447;