5-80571390-G-T

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 0.542 in 151,950 control chromosomes in the GnomAD database, including 24,218 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 0.54 (24218 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.418

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.934 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: 0.542 AC: 82317 AN: 151832 Hom.: 24204 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.633

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.957

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.542 AC: 82347 AN: 151950 Hom.: 24218 Cov.: 32 AF XY: 0.550 AC XY: 40811 AN XY: 74260

Gnomad4 AFR AF: 0.314

Gnomad4 AMR AF: 0.659

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.957

Gnomad4 SAS AF: 0.568

Gnomad4 FIN AF: 0.697

Gnomad4 NFE AF: 0.591

Gnomad4 OTH AF: 0.546

Alfa AF: 0.587 Hom.: 50944

Bravo AF: 0.533

Asia WGS AF: 0.718 AC: 2494 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.36
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs249209; hg19: chr5-79867209;