rs6827285

chr4-160183148-G-A

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 0.265 in 151,702 control chromosomes in the GnomAD database, including 5,934 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 0.26 (5934 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.370

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40142 AN: 151584 Hom.: 5920 Cov.: 32

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.0864

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.265 AC: 40196 AN: 151702 Hom.: 5934 Cov.: 32 AF XY: 0.258 AC XY: 19117 AN XY: 74136

Gnomad4 AFR AF: 0.402

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.0862

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.231

Alfa AF: 0.238 Hom.: 1086

Bravo AF: 0.272

Asia WGS AF: 0.128 AC: 444 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.9
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6827285; hg19: chr4-161104300; COSMIC: COSV67093145;