5-99833655-C-T

Variant names:

• chr5-99833655-C-T
• rs6888673

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 0.737 in 151,684 control chromosomes in the GnomAD database, including 41,373 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 0.74 (41373 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.553

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.736 AC: 111611 AN: 151566 Hom.: 41327 Cov.: 30

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.741

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

GnomAD4 genome AF: 0.737 AC: 111716 AN: 151684 Hom.: 41373 Cov.: 30 AF XY: 0.737 AC XY: 54626 AN XY: 74124

Gnomad4 AFR AF: 0.830

Gnomad4 AMR AF: 0.721

Gnomad4 ASJ AF: 0.817

Gnomad4 EAS AF: 0.640

Gnomad4 SAS AF: 0.726

Gnomad4 FIN AF: 0.710

Gnomad4 NFE AF: 0.692

Gnomad4 OTH AF: 0.742

Alfa AF: 0.711 Hom.: 9591

Bravo AF: 0.742

Asia WGS AF: 0.711 AC: 2474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.89
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: rs6888673; hg19: chr5-99169359;