1-22159378-T-G

Variant names:

• chr1-22159378-T-G
• rs16826658

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 0.326 in 152,046 control chromosomes in the GnomAD database, including 8,750 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 0.33 (8750 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.284
• Publications: 41 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.491 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: 0.326 AC: 49518 AN: 151928 Hom.: 8737 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.326 AC: 49562 AN: 152046 Hom.: 8750 Cov.: 32 AF XY: 0.329 AC XY: 24434 AN XY: 74336

African (AFR) AF: 0.184 AC: 7613 AN: 41480

American (AMR) AF: 0.351 AC: 5357 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 978 AN: 3472

East Asian (EAS) AF: 0.507 AC: 2619 AN: 5164

South Asian (SAS) AF: 0.395 AC: 1903 AN: 4814

European-Finnish (FIN) AF: 0.331 AC: 3497 AN: 10576

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.389 AC: 26412 AN: 67944

Other (OTH) AF: 0.318 AC: 673 AN: 2116

Alfa AF: 0.370 Hom.: 29242

Bravo AF: 0.321

Asia WGS AF: 0.425 AC: 1478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.6
DANN	Benign	0.44
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs16826658; hg19: chr1-22485871;