5-56808481-A-G

Position:

• chr5-56808481-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 0.754 in 149,348 control chromosomes in the GnomAD database, including 42,427 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 0.75 (42427 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

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 (NFE) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.754 AC: 112471 AN: 149238 Hom.: 42398 Cov.: 31

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.771

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.820

Gnomad OTH AF: 0.754

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

GnomAD4 genome AF: 0.754 AC: 112546 AN: 149348 Hom.: 42427 Cov.: 31 AF XY: 0.749 AC XY: 54773 AN XY: 73094

Gnomad4 AFR AF: 0.671

Gnomad4 AMR AF: 0.670

Gnomad4 ASJ AF: 0.817

Gnomad4 EAS AF: 0.580

Gnomad4 SAS AF: 0.771

Gnomad4 FIN AF: 0.809

Gnomad4 NFE AF: 0.820

Gnomad4 OTH AF: 0.756

Alfa AF: 0.782 Hom.: 27184

Bravo AF: 0.724

Asia WGS AF: 0.690 AC: 2400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.69
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10461617; hg19: chr5-56104308;