5-16286654-T-C

Position:

• chr5-16286654-T-C

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 0.807 in 152,134 control chromosomes in the GnomAD database, including 49,686 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 0.81 (49686 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.361

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.819 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: 0.807 AC: 122691 AN: 152016 Hom.: 49671 Cov.: 32

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.782

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.835

Gnomad FIN AF: 0.897

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.780

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

GnomAD4 genome AF: 0.807 AC: 122752 AN: 152134 Hom.: 49686 Cov.: 32 AF XY: 0.810 AC XY: 60251 AN XY: 74342

Gnomad4 AFR AF: 0.780

Gnomad4 AMR AF: 0.760

Gnomad4 ASJ AF: 0.782

Gnomad4 EAS AF: 0.765

Gnomad4 SAS AF: 0.834

Gnomad4 FIN AF: 0.897

Gnomad4 NFE AF: 0.825

Gnomad4 OTH AF: 0.780

Alfa AF: 0.809 Hom.: 12591

Bravo AF: 0.791

Asia WGS AF: 0.767 AC: 2667 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.9
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs860545; hg19: chr5-16286763;