chr5-141831188-A-G

Variant names:

• chr5-141831188-A-G
• rs166040

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 0.82 in 152,206 control chromosomes in the GnomAD database, including 51,588 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 0.82 (51588 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.431
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.875 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: 0.820 AC: 124689 AN: 152088 Hom.: 51567 Cov.: 32

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.889

Gnomad AMR AF: 0.735

Gnomad ASJ AF: 0.847

Gnomad EAS AF: 0.828

Gnomad SAS AF: 0.813

Gnomad FIN AF: 0.909

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.881

Gnomad OTH AF: 0.825

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

GnomAD4 genome AF: 0.820 AC: 124753 AN: 152206 Hom.: 51588 Cov.: 32 AF XY: 0.817 AC XY: 60789 AN XY: 74404

African (AFR) AF: 0.723 AC: 30031 AN: 41512

American (AMR) AF: 0.734 AC: 11227 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.847 AC: 2938 AN: 3470

East Asian (EAS) AF: 0.828 AC: 4277 AN: 5168

South Asian (SAS) AF: 0.813 AC: 3921 AN: 4820

European-Finnish (FIN) AF: 0.909 AC: 9636 AN: 10600

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.881 AC: 59917 AN: 68022

Other (OTH) AF: 0.826 AC: 1747 AN: 2114

Alfa AF: 0.851 Hom.: 167684

Bravo AF: 0.804

Asia WGS AF: 0.839 AC: 2919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.2
DANN	Benign	0.65
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs166040; hg19: chr5-141210753;