1-55021673-C-G

Variant names:

• chr1-55021673-C-G
• rs12117661

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 0.274 in 151,958 control chromosomes in the GnomAD database, including 6,227 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 0.27 (6227 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.994
• Publications: 28 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 (AFR) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41642 AN: 151840 Hom.: 6220 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.274 AC: 41674 AN: 151958 Hom.: 6227 Cov.: 32 AF XY: 0.271 AC XY: 20116 AN XY: 74276

African (AFR) AF: 0.394 AC: 16340 AN: 41420

American (AMR) AF: 0.188 AC: 2876 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 812 AN: 3472

East Asian (EAS) AF: 0.140 AC: 720 AN: 5152

South Asian (SAS) AF: 0.168 AC: 808 AN: 4810

European-Finnish (FIN) AF: 0.248 AC: 2625 AN: 10568

Middle Eastern (MID) AF: 0.226 AC: 66 AN: 292

European-Non Finnish (NFE) AF: 0.243 AC: 16487 AN: 67938

Other (OTH) AF: 0.263 AC: 556 AN: 2112

Alfa AF: 0.137 Hom.: 234

Bravo AF: 0.280

Asia WGS AF: 0.192 AC: 669 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	3.8
DANN	Benign	0.84
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs12117661; hg19: chr1-55487346;