5-175439295-A-G

Position:

• chr5-175439295-A-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 0.613 in 152,040 control chromosomes in the GnomAD database, including 29,043 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 0.61 (29043 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.492

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.84 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.175439295A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93191 AN: 151922 Hom.: 29032 Cov.: 32

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.861

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.613 AC: 93248 AN: 152040 Hom.: 29043 Cov.: 32 AF XY: 0.617 AC XY: 45874 AN XY: 74314

Gnomad4 AFR AF: 0.536

Gnomad4 AMR AF: 0.696

Gnomad4 ASJ AF: 0.685

Gnomad4 EAS AF: 0.861

Gnomad4 SAS AF: 0.594

Gnomad4 FIN AF: 0.624

Gnomad4 NFE AF: 0.619

Gnomad4 OTH AF: 0.649

Alfa AF: 0.329 Hom.: 3526

Bravo AF: 0.620

Asia WGS AF: 0.706 AC: 2454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.9
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11749676; hg19: chr5-174866298; COSMIC: COSV67104355;