5-11929801-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 0.496 in 152,048 control chromosomes in the GnomAD database, including 19,807 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 0.50 (19807 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.605

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 (EAS) allele frequency at 95% confidence interval = 0.805 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: 0.495 AC: 75261 AN: 151930 Hom.: 19766 Cov.: 32

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.496 AC: 75359 AN: 152048 Hom.: 19807 Cov.: 32 AF XY: 0.500 AC XY: 37124 AN XY: 74320

Gnomad4 AFR AF: 0.631

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.826

Gnomad4 SAS AF: 0.601

Gnomad4 FIN AF: 0.379

Gnomad4 NFE AF: 0.404

Gnomad4 OTH AF: 0.466

Alfa AF: 0.426 Hom.: 18983

Bravo AF: 0.513

Asia WGS AF: 0.688 AC: 2388 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	0.18
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6884647; hg19: chr5-11929913;