rs6836146

Variant names:

• chr4-179658291-A-C
• rs6836146

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.0984

Gnomad4 ASJ AF: 0.0130

Gnomad4 EAS AF: 0.285

Gnomad4 SAS AF: 0.0633

Gnomad4 FIN AF: 0.0572

Gnomad4 NFE AF: 0.0202

Gnomad4 OTH AF: 0.0450

Alfa AF: 0.0315 Hom.: 450

Bravo AF: 0.0765

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6836146; hg19: chr4-180579444;