5-56510924-A-G

Variant names:

• chr5-56510924-A-G
• rs459193

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 0.684 in 152,088 control chromosomes in the GnomAD database, including 36,065 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 0.68 (36065 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.684 AC: 103995 AN: 151968 Hom.: 36054 Cov.: 32

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.691

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

GnomAD4 genome AF: 0.684 AC: 104045 AN: 152088 Hom.: 36065 Cov.: 32 AF XY: 0.681 AC XY: 50602 AN XY: 74338

Gnomad4 AFR AF: 0.582

Gnomad4 AMR AF: 0.750

Gnomad4 ASJ AF: 0.814

Gnomad4 EAS AF: 0.500

Gnomad4 SAS AF: 0.629

Gnomad4 FIN AF: 0.676

Gnomad4 NFE AF: 0.743

Gnomad4 OTH AF: 0.684

Alfa AF: 0.726 Hom.: 46597

Bravo AF: 0.685

Asia WGS AF: 0.527 AC: 1836 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.32
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs459193; hg19: chr5-55806751;