1-199473184-G-A

Variant names:

• chr1-199473184-G-A
• rs10494793

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.183 in 151,824 control chromosomes in the GnomAD database, including 2,640 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 0.18 (2640 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.28
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27787 AN: 151704 Hom.: 2636 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.183 AC: 27805 AN: 151824 Hom.: 2640 Cov.: 32 AF XY: 0.185 AC XY: 13722 AN XY: 74218

African (AFR) AF: 0.169 AC: 6988 AN: 41452

American (AMR) AF: 0.158 AC: 2411 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 631 AN: 3470

East Asian (EAS) AF: 0.335 AC: 1716 AN: 5130

South Asian (SAS) AF: 0.152 AC: 731 AN: 4810

European-Finnish (FIN) AF: 0.215 AC: 2267 AN: 10566

Middle Eastern (MID) AF: 0.164 AC: 48 AN: 292

European-Non Finnish (NFE) AF: 0.184 AC: 12513 AN: 67872

Other (OTH) AF: 0.177 AC: 373 AN: 2108

Alfa AF: 0.184 Hom.: 10095

Bravo AF: 0.181

Asia WGS AF: 0.254 AC: 880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	18
DANN	Benign	0.81
PhyloP100		2.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10494793; hg19: chr1-199442312;