1-203190578-A-G

Variant names:

• chr1-203190578-A-G
• rs2364574

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 0.0764 in 152,222 control chromosomes in the GnomAD database, including 785 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 0.076 (785 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.26 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: 0.0761 AC: 11579 AN: 152104 Hom.: 767 Cov.: 33

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.0885

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.0137

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0336

Gnomad OTH AF: 0.0927

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

GnomAD4 genome AF: 0.0764 AC: 11630 AN: 152222 Hom.: 785 Cov.: 33 AF XY: 0.0789 AC XY: 5876 AN XY: 74440

African (AFR) AF: 0.108 AC: 4489 AN: 41518

American (AMR) AF: 0.139 AC: 2134 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0885 AC: 307 AN: 3470

East Asian (EAS) AF: 0.272 AC: 1409 AN: 5178

South Asian (SAS) AF: 0.117 AC: 566 AN: 4828

European-Finnish (FIN) AF: 0.0137 AC: 145 AN: 10610

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0336 AC: 2286 AN: 68000

Other (OTH) AF: 0.100 AC: 212 AN: 2114

Alfa AF: 0.0839 Hom.: 307

Bravo AF: 0.0920

Asia WGS AF: 0.200 AC: 693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.6
DANN	Benign	0.51
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs2364574; hg19: chr1-203159706;