2-6800825-C-T

Variant names:

• chr2-6800825-C-T
• rs1505694

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 0.46 in 152,094 control chromosomes in the GnomAD database, including 17,996 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 0.46 (17996 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.7 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: 0.460 AC: 69931 AN: 151976 Hom.: 17941 Cov.: 33

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.460 AC: 70037 AN: 152094 Hom.: 17996 Cov.: 33 AF XY: 0.464 AC XY: 34473 AN XY: 74354

African (AFR) AF: 0.707 AC: 29315 AN: 41478

American (AMR) AF: 0.444 AC: 6784 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1617 AN: 3466

East Asian (EAS) AF: 0.397 AC: 2053 AN: 5170

South Asian (SAS) AF: 0.439 AC: 2119 AN: 4822

European-Finnish (FIN) AF: 0.369 AC: 3903 AN: 10578

Middle Eastern (MID) AF: 0.486 AC: 142 AN: 292

European-Non Finnish (NFE) AF: 0.336 AC: 22858 AN: 67984

Other (OTH) AF: 0.466 AC: 985 AN: 2112

Alfa AF: 0.421 Hom.: 1941

Bravo AF: 0.473

Asia WGS AF: 0.467 AC: 1621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.043
DANN	Benign	0.41
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1505694; hg19: chr2-6940956;