1-221479161-T-G

Variant names:

• chr1-221479161-T-G
• rs1903138

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 0.217 in 152,084 control chromosomes in the GnomAD database, including 4,427 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 (4427 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.395
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33055 AN: 151966 Hom.: 4425 Cov.: 32

Gnomad AFR AF: 0.0556

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.217 AC: 33062 AN: 152084 Hom.: 4427 Cov.: 32 AF XY: 0.222 AC XY: 16526 AN XY: 74326

African (AFR) AF: 0.0554 AC: 2301 AN: 41524

American (AMR) AF: 0.259 AC: 3952 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 843 AN: 3460

East Asian (EAS) AF: 0.345 AC: 1781 AN: 5156

South Asian (SAS) AF: 0.238 AC: 1149 AN: 4824

European-Finnish (FIN) AF: 0.339 AC: 3576 AN: 10556

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18748 AN: 67966

Other (OTH) AF: 0.230 AC: 485 AN: 2112

Alfa AF: 0.253 Hom.: 15074

Bravo AF: 0.205

Asia WGS AF: 0.289 AC: 1002 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	3.1
DANN	Benign	0.64
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs1903138; hg19: chr1-221652503;