5-175433696-T-C

Position:

• chr5-175433696-T-C

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 0.572 in 152,026 control chromosomes in the GnomAD database, including 25,099 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 0.57 (25099 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0120

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.175433696T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.572 AC: 86849 AN: 151908 Hom.: 25076 Cov.: 32

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.572 AC: 86919 AN: 152026 Hom.: 25099 Cov.: 32 AF XY: 0.571 AC XY: 42416 AN XY: 74320

Gnomad4 AFR AF: 0.629

Gnomad4 AMR AF: 0.620

Gnomad4 ASJ AF: 0.598

Gnomad4 EAS AF: 0.558

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.547

Gnomad4 OTH AF: 0.586

Alfa AF: 0.555 Hom.: 42371

Bravo AF: 0.585

Asia WGS AF: 0.476 AC: 1653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.9
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs265973; hg19: chr5-174860699; COSMIC: COSV60236681;