5-172724078-A-G

Position:

• chr5-172724078-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 0.904 in 152,234 control chromosomes in the GnomAD database, including 62,539 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 0.90 (62539 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.211

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.172724078A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.904 AC: 137557 AN: 152116 Hom.: 62490 Cov.: 31

Gnomad AFR AF: 0.970

Gnomad AMI AF: 0.947

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.913

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.887

Gnomad FIN AF: 0.869

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.902

Gnomad OTH AF: 0.912

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

GnomAD4 genome AF: 0.904 AC: 137662 AN: 152234 Hom.: 62539 Cov.: 31 AF XY: 0.899 AC XY: 66931 AN XY: 74428

Gnomad4 AFR AF: 0.969

Gnomad4 AMR AF: 0.812

Gnomad4 ASJ AF: 0.913

Gnomad4 EAS AF: 0.751

Gnomad4 SAS AF: 0.886

Gnomad4 FIN AF: 0.869

Gnomad4 NFE AF: 0.902

Gnomad4 OTH AF: 0.912

Alfa AF: 0.883 Hom.: 6566

Bravo AF: 0.902

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.6
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2618346; hg19: chr5-172151081;