5-177086459-A-G

Position:

• chr5-177086459-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 0.634 in 151,770 control chromosomes in the GnomAD database, including 32,127 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 0.63 (32127 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.686

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 (EAS) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96136 AN: 151652 Hom.: 32118 Cov.: 29

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.974

Gnomad SAS AF: 0.858

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.634

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

GnomAD4 genome AF: 0.634 AC: 96181 AN: 151770 Hom.: 32127 Cov.: 29 AF XY: 0.642 AC XY: 47590 AN XY: 74156

Gnomad4 AFR AF: 0.418

Gnomad4 AMR AF: 0.712

Gnomad4 ASJ AF: 0.686

Gnomad4 EAS AF: 0.974

Gnomad4 SAS AF: 0.860

Gnomad4 FIN AF: 0.733

Gnomad4 NFE AF: 0.688

Gnomad4 OTH AF: 0.633

Alfa AF: 0.664 Hom.: 8660

Bravo AF: 0.620

Asia WGS AF: 0.846 AC: 2940 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.9
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs641101; hg19: chr5-176513460;