chr6-86059571-C-A

Position:

• chr6-86059571-C-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 0.235 in 151,528 control chromosomes in the GnomAD database, including 5,117 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 0.23 (5117 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.986

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.323 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: 0.235 AC: 35580 AN: 151412 Hom.: 5117 Cov.: 31

Gnomad AFR AF: 0.0844

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.235 AC: 35578 AN: 151528 Hom.: 5117 Cov.: 31 AF XY: 0.233 AC XY: 17270 AN XY: 73992

Gnomad4 AFR AF: 0.0843

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.336

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.358

Gnomad4 NFE AF: 0.321

Gnomad4 OTH AF: 0.227

Alfa AF: 0.277 Hom.: 806

Bravo AF: 0.214

Asia WGS AF: 0.227 AC: 788 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	11
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12665321; hg19: chr6-86769289;