rs1890133

Variant names:

• chr1-199485750-G-A
• rs1890133

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 0.247 in 151,614 control chromosomes in the GnomAD database, including 4,738 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 0.25 (4738 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.168
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.279 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: 0.247 AC: 37451 AN: 151496 Hom.: 4724 Cov.: 31

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.0899

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.247 AC: 37515 AN: 151614 Hom.: 4738 Cov.: 31 AF XY: 0.244 AC XY: 18095 AN XY: 74078

African (AFR) AF: 0.281 AC: 11618 AN: 41358

American (AMR) AF: 0.286 AC: 4342 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 585 AN: 3466

East Asian (EAS) AF: 0.141 AC: 726 AN: 5134

South Asian (SAS) AF: 0.0910 AC: 438 AN: 4812

European-Finnish (FIN) AF: 0.246 AC: 2595 AN: 10540

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16424 AN: 67816

Other (OTH) AF: 0.224 AC: 472 AN: 2108

Alfa AF: 0.239 Hom.: 7292

Bravo AF: 0.257

Asia WGS AF: 0.137 AC: 478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.7
DANN	Benign	0.20
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs1890133; hg19: chr1-199454878;