rs6836146

Positions:

• chr4-179658291-A-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;