chr1-22689610-T-C

Variant names:

• chr1-22689610-T-C
• rs17433871

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 0.225 in 151,846 control chromosomes in the GnomAD database, including 4,069 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 0.22 (4069 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.654
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.269 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: 0.225 AC: 34132 AN: 151728 Hom.: 4064 Cov.: 31

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.225 AC: 34151 AN: 151846 Hom.: 4069 Cov.: 31 AF XY: 0.220 AC XY: 16339 AN XY: 74196

African (AFR) AF: 0.156 AC: 6455 AN: 41400

American (AMR) AF: 0.210 AC: 3197 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 907 AN: 3466

East Asian (EAS) AF: 0.155 AC: 799 AN: 5158

South Asian (SAS) AF: 0.159 AC: 764 AN: 4802

European-Finnish (FIN) AF: 0.268 AC: 2816 AN: 10524

Middle Eastern (MID) AF: 0.192 AC: 56 AN: 292

European-Non Finnish (NFE) AF: 0.272 AC: 18475 AN: 67950

Other (OTH) AF: 0.250 AC: 527 AN: 2106

Alfa AF: 0.256 Hom.: 11235

Bravo AF: 0.220

Asia WGS AF: 0.221 AC: 771 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.8
DANN	Benign	0.62
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs17433871; hg19: chr1-23016103;