rs6866893

Variant names:

• chr5-34551654-C-T
• rs6866893

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 0.691 in 152,084 control chromosomes in the GnomAD database, including 36,913 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 0.69 (36913 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.815

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.759 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: 0.691 AC: 105075 AN: 151966 Hom.: 36908 Cov.: 33

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.760

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.792

Gnomad EAS AF: 0.660

Gnomad SAS AF: 0.597

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.706

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

GnomAD4 genome AF: 0.691 AC: 105110 AN: 152084 Hom.: 36913 Cov.: 33 AF XY: 0.685 AC XY: 50897 AN XY: 74334

Gnomad4 AFR AF: 0.565

Gnomad4 AMR AF: 0.737

Gnomad4 ASJ AF: 0.792

Gnomad4 EAS AF: 0.660

Gnomad4 SAS AF: 0.597

Gnomad4 FIN AF: 0.661

Gnomad4 NFE AF: 0.765

Gnomad4 OTH AF: 0.701

Alfa AF: 0.711 Hom.: 4836

Bravo AF: 0.695

Asia WGS AF: 0.611 AC: 2130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.9
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6866893; hg19: chr5-34551759;