5-179509721-A-G

Position:

• chr5-179509721-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 0.282 in 151,678 control chromosomes in the GnomAD database, including 7,717 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 0.28 (7717 hom., cov: 32)
• Consequence: LOC100128622 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.626

Genes affected

LOC100128622 (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 (EAS) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100128622		n.179509721A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000253652	ENST00000520758.1	n.116+5743T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42754 AN: 151562 Hom.: 7684 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.282 AC: 42839 AN: 151678 Hom.: 7717 Cov.: 32 AF XY: 0.290 AC XY: 21476 AN XY: 74108

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.449

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.615

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.283

Alfa AF: 0.209 Hom.: 9462

Bravo AF: 0.309

Asia WGS AF: 0.483 AC: 1676 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9329079; hg19: chr5-178936722;