1-221479161-T-G

Position:

• chr1-221479161-T-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.0554

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.339

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.230

Alfa AF: 0.266 Hom.: 11078

Bravo AF: 0.205

Asia WGS AF: 0.289 AC: 1002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.1
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1903138; hg19: chr1-221652503;