1-22680682-C-T

Variant names:

• chr1-22680682-C-T
• rs17486657

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 0.286 in 152,086 control chromosomes in the GnomAD database, including 6,324 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 0.29 (6324 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.568
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.308 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: 0.286 AC: 43452 AN: 151968 Hom.: 6326 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.286 AC: 43453 AN: 152086 Hom.: 6324 Cov.: 32 AF XY: 0.285 AC XY: 21186 AN XY: 74334

African (AFR) AF: 0.240 AC: 9943 AN: 41480

American (AMR) AF: 0.310 AC: 4738 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1167 AN: 3468

East Asian (EAS) AF: 0.204 AC: 1058 AN: 5178

South Asian (SAS) AF: 0.208 AC: 1005 AN: 4826

European-Finnish (FIN) AF: 0.313 AC: 3301 AN: 10552

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.312 AC: 21185 AN: 67986

Other (OTH) AF: 0.282 AC: 595 AN: 2108

Alfa AF: 0.301 Hom.: 27611

Bravo AF: 0.283

Asia WGS AF: 0.202 AC: 703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.91
DANN	Benign	0.21
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs17486657; hg19: chr1-23007175; COSMIC: COSV59931309;