chr1-90460425-C-A

Variant names:

• chr1-90460425-C-A
• rs2136094

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 0.29 in 151,254 control chromosomes in the GnomAD database, including 6,565 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 (6565 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.126
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.38 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: 0.290 AC: 43799 AN: 151134 Hom.: 6554 Cov.: 30

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.290 AC: 43835 AN: 151254 Hom.: 6565 Cov.: 30 AF XY: 0.291 AC XY: 21516 AN XY: 73822

African (AFR) AF: 0.358 AC: 14721 AN: 41166

American (AMR) AF: 0.230 AC: 3499 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 807 AN: 3468

East Asian (EAS) AF: 0.395 AC: 2014 AN: 5102

South Asian (SAS) AF: 0.378 AC: 1809 AN: 4788

European-Finnish (FIN) AF: 0.307 AC: 3200 AN: 10420

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.252 AC: 17089 AN: 67820

Other (OTH) AF: 0.261 AC: 547 AN: 2094

Alfa AF: 0.262 Hom.: 3115

Bravo AF: 0.283

Asia WGS AF: 0.393 AC: 1362 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.9
DANN	Benign	0.39
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs2136094; hg19: chr1-90925982;