rs6866893

Variant names:

• chr5-34551654-C-T
• rs6866893

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.565 AC: 23419 AN: 41460

American (AMR) AF: 0.737 AC: 11271 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.792 AC: 2748 AN: 3470

East Asian (EAS) AF: 0.660 AC: 3411 AN: 5166

South Asian (SAS) AF: 0.597 AC: 2881 AN: 4824

European-Finnish (FIN) AF: 0.661 AC: 6984 AN: 10560

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.765 AC: 51993 AN: 68000

Other (OTH) AF: 0.701 AC: 1481 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.9
DANN	Benign	0.64
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs6866893; hg19: chr5-34551759;