1-22355873-C-T

Variant names:

• chr1-22355873-C-T
• rs12742784

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 0.255 in 151,828 control chromosomes in the GnomAD database, including 5,515 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 0.26 (5515 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.352 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: 0.255 AC: 38698 AN: 151710 Hom.: 5514 Cov.: 31

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.255 AC: 38724 AN: 151828 Hom.: 5515 Cov.: 31 AF XY: 0.254 AC XY: 18811 AN XY: 74180

African (AFR) AF: 0.357 AC: 14755 AN: 41346

American (AMR) AF: 0.250 AC: 3819 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 768 AN: 3466

East Asian (EAS) AF: 0.365 AC: 1879 AN: 5146

South Asian (SAS) AF: 0.360 AC: 1730 AN: 4810

European-Finnish (FIN) AF: 0.124 AC: 1311 AN: 10554

Middle Eastern (MID) AF: 0.305 AC: 89 AN: 292

European-Non Finnish (NFE) AF: 0.201 AC: 13650 AN: 67950

Other (OTH) AF: 0.247 AC: 520 AN: 2104

Alfa AF: 0.218 Hom.: 9192

Bravo AF: 0.267

Asia WGS AF: 0.361 AC: 1257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.3
DANN	Benign	0.77
PhyloP100		0.060

Splicing

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

Other links and lift over

dbSNP: rs12742784; hg19: chr1-22682366;