5-135016844-C-T

Position:

• chr5-135016844-C-T

Variant summary

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

The variant allele was found at a frequency of 0.402 in 152,088 control chromosomes in the GnomAD database, including 13,092 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 0.40 (13092 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.386

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.135016844C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61017 AN: 151970 Hom.: 13063 Cov.: 33

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.402 AC: 61067 AN: 152088 Hom.: 13092 Cov.: 33 AF XY: 0.405 AC XY: 30141 AN XY: 74358

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.519

Gnomad4 ASJ AF: 0.353

Gnomad4 EAS AF: 0.623

Gnomad4 SAS AF: 0.599

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.393

Alfa AF: 0.421 Hom.: 23014

Bravo AF: 0.402

Asia WGS AF: 0.619 AC: 2149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.8
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28330; hg19: chr5-134352534; COSMIC: COSV60199531;