5-56764568-T-A

Position:

• chr5-56764568-T-A

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 0.235 in 152,202 control chromosomes in the GnomAD database, including 5,555 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 0.23 (5555 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.343 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: 0.235 AC: 35732 AN: 152084 Hom.: 5557 Cov.: 32

Gnomad AFR AF: 0.0680

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.00923

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.235 AC: 35714 AN: 152202 Hom.: 5555 Cov.: 32 AF XY: 0.226 AC XY: 16845 AN XY: 74420

Gnomad4 AFR AF: 0.0679

Gnomad4 AMR AF: 0.216

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.00906

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.280

Alfa AF: 0.262 Hom.: 676

Bravo AF: 0.225

Asia WGS AF: 0.0760 AC: 263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.1
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1895452; hg19: chr5-56060395; COSMIC: COSV60135531;