5-8092964-C-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 0.594 in 152,030 control chromosomes in the GnomAD database, including 27,580 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 0.59 (27580 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.89 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: 0.594 AC: 90213 AN: 151914 Hom.: 27571 Cov.: 33

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.912

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.594 AC: 90254 AN: 152030 Hom.: 27580 Cov.: 33 AF XY: 0.602 AC XY: 44763 AN XY: 74310

Gnomad4 AFR AF: 0.475

Gnomad4 AMR AF: 0.640

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.912

Gnomad4 SAS AF: 0.670

Gnomad4 FIN AF: 0.665

Gnomad4 NFE AF: 0.613

Gnomad4 OTH AF: 0.607

Alfa AF: 0.598 Hom.: 13112

Bravo AF: 0.588

Asia WGS AF: 0.765 AC: 2663 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.1
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10475407; hg19: chr5-8093077;