5-175432494-C-G

Position:

• chr5-175432494-C-G

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 0.169 in 152,208 control chromosomes in the GnomAD database, including 2,260 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 0.17 (2260 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.175432494C>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25783 AN: 152090 Hom.: 2259 Cov.: 33

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.0824

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.169 AC: 25786 AN: 152208 Hom.: 2260 Cov.: 33 AF XY: 0.170 AC XY: 12681 AN XY: 74410

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.175

Alfa AF: 0.160 Hom.: 1149

Bravo AF: 0.174

Asia WGS AF: 0.130 AC: 453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11742274; hg19: chr5-174859497;