1-22204641-C-T

Position:

• chr1-22204641-C-T

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 0.0637 in 152,228 control chromosomes in the GnomAD database, including 438 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 0.064 (438 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.896

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0943 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: 0.0639 AC: 9713 AN: 152110 Hom.: 439 Cov.: 33

Gnomad AFR AF: 0.0173

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.0695

Gnomad ASJ AF: 0.0903

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0307

Gnomad FIN AF: 0.0631

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0963

Gnomad OTH AF: 0.0793

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

GnomAD4 genome AF: 0.0637 AC: 9703 AN: 152228 Hom.: 438 Cov.: 33 AF XY: 0.0615 AC XY: 4578 AN XY: 74428

Gnomad4 AFR AF: 0.0173

Gnomad4 AMR AF: 0.0695

Gnomad4 ASJ AF: 0.0903

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0303

Gnomad4 FIN AF: 0.0631

Gnomad4 NFE AF: 0.0962

Gnomad4 OTH AF: 0.0780

Alfa AF: 0.0750 Hom.: 66

Bravo AF: 0.0615

Asia WGS AF: 0.0150 AC: 52 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	15
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs926435; hg19: chr1-22531134;