rs2179555

Variant names:

• chr1-186684944-T-C
• rs2179555

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 0.196 in 152,062 control chromosomes in the GnomAD database, including 3,840 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 0.20 (3840 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.358 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: 0.196 AC: 29761 AN: 151944 Hom.: 3809 Cov.: 32

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.0469

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.0717

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.196 AC: 29841 AN: 152062 Hom.: 3840 Cov.: 32 AF XY: 0.191 AC XY: 14172 AN XY: 74340

African (AFR) AF: 0.363 AC: 15036 AN: 41432

American (AMR) AF: 0.166 AC: 2535 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 717 AN: 3470

East Asian (EAS) AF: 0.0466 AC: 241 AN: 5170

South Asian (SAS) AF: 0.174 AC: 840 AN: 4824

European-Finnish (FIN) AF: 0.0717 AC: 759 AN: 10588

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9187 AN: 67980

Other (OTH) AF: 0.207 AC: 436 AN: 2108

Alfa AF: 0.166 Hom.: 2987

Bravo AF: 0.210

Asia WGS AF: 0.169 AC: 590 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.35
DANN	Benign	0.48
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs2179555; hg19: chr1-186654076;