5-179010189-G-A

Variant names:

• chr5-179010189-G-A
• rs1845940

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 0.233 in 151,912 control chromosomes in the GnomAD database, including 5,180 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 0.23 (5180 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.739
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35417 AN: 151794 Hom.: 5178 Cov.: 33

Gnomad AFR AF: 0.0553

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.233 AC: 35422 AN: 151912 Hom.: 5180 Cov.: 33 AF XY: 0.236 AC XY: 17547 AN XY: 74244

African (AFR) AF: 0.0554 AC: 2299 AN: 41476

American (AMR) AF: 0.276 AC: 4207 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1259 AN: 3470

East Asian (EAS) AF: 0.287 AC: 1482 AN: 5164

South Asian (SAS) AF: 0.410 AC: 1972 AN: 4814

European-Finnish (FIN) AF: 0.269 AC: 2824 AN: 10516

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.298 AC: 20232 AN: 67898

Other (OTH) AF: 0.269 AC: 565 AN: 2100

Alfa AF: 0.290 Hom.: 3287

Bravo AF: 0.222

Asia WGS AF: 0.315 AC: 1086 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	3.9
DANN	Benign	0.72
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs1845940; hg19: chr5-178437190;