rs3829793

Variant names:

• chr1-161224610-C-G
• rs3829793

Your query was ambiguous. Multiple possible variants found:

• chr1-161224610-C-G
• chr1-161224610-C-T

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 152,110 control chromosomes in the GnomAD database, including 7,372 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 (7372 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.225
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.521 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: 0.291 AC: 44173 AN: 151992 Hom.: 7372 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.290 AC: 44180 AN: 152110 Hom.: 7372 Cov.: 32 AF XY: 0.291 AC XY: 21672 AN XY: 74352

African (AFR) AF: 0.123 AC: 5090 AN: 41514

American (AMR) AF: 0.361 AC: 5529 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1079 AN: 3468

East Asian (EAS) AF: 0.538 AC: 2778 AN: 5168

South Asian (SAS) AF: 0.315 AC: 1517 AN: 4820

European-Finnish (FIN) AF: 0.314 AC: 3323 AN: 10574

Middle Eastern (MID) AF: 0.277 AC: 81 AN: 292

European-Non Finnish (NFE) AF: 0.350 AC: 23811 AN: 67952

Other (OTH) AF: 0.310 AC: 653 AN: 2106

Alfa AF: 0.173 Hom.: 366

Bravo AF: 0.288

Asia WGS AF: 0.436 AC: 1514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.34
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs3829793; hg19: chr1-161194400;