rs6836146

Variant names:

• chr4-179658291-A-C
• rs6836146

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 0.0661 in 152,242 control chromosomes in the GnomAD database, including 647 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 0.066 (647 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.558
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.273 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: 0.0660 AC: 10044 AN: 152124 Hom.: 645 Cov.: 33

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0977

Gnomad ASJ AF: 0.0130

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.0626

Gnomad FIN AF: 0.0572

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0202

Gnomad OTH AF: 0.0445

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

GnomAD4 genome AF: 0.0661 AC: 10058 AN: 152242 Hom.: 647 Cov.: 33 AF XY: 0.0692 AC XY: 5151 AN XY: 74440

African (AFR) AF: 0.111 AC: 4627 AN: 41542

American (AMR) AF: 0.0984 AC: 1503 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0130 AC: 45 AN: 3470

East Asian (EAS) AF: 0.285 AC: 1472 AN: 5168

South Asian (SAS) AF: 0.0633 AC: 305 AN: 4822

European-Finnish (FIN) AF: 0.0572 AC: 607 AN: 10616

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0202 AC: 1372 AN: 68024

Other (OTH) AF: 0.0450 AC: 95 AN: 2112

Alfa AF: 0.0380 Hom.: 898

Bravo AF: 0.0765

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.4
DANN	Benign	0.43
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs6836146; hg19: chr4-180579444;