1-182569447-C-G

Variant names:

• chr1-182569447-C-G
• rs12723593

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 0.292 in 151,570 control chromosomes in the GnomAD database, including 6,835 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 0.29 (6835 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.888
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.343 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: 0.292 AC: 44259 AN: 151452 Hom.: 6825 Cov.: 29

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.00502

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.292 AC: 44305 AN: 151570 Hom.: 6835 Cov.: 29 AF XY: 0.290 AC XY: 21507 AN XY: 74048

African (AFR) AF: 0.348 AC: 14365 AN: 41270

American (AMR) AF: 0.251 AC: 3815 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 665 AN: 3470

East Asian (EAS) AF: 0.00503 AC: 26 AN: 5164

South Asian (SAS) AF: 0.162 AC: 779 AN: 4800

European-Finnish (FIN) AF: 0.349 AC: 3655 AN: 10460

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.297 AC: 20154 AN: 67888

Other (OTH) AF: 0.277 AC: 583 AN: 2102

Alfa AF: 0.191 Hom.: 413

Bravo AF: 0.286

Asia WGS AF: 0.114 AC: 399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.58
DANN	Benign	0.53
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs12723593; hg19: chr1-182538582;