chr6-86234881-G-A

Position:

• chr6-86234881-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 0.593 in 151,974 control chromosomes in the GnomAD database, including 26,882 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 0.59 (26882 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.620

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.631 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: 0.593 AC: 90036 AN: 151854 Hom.: 26856 Cov.: 32

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.593 AC: 90122 AN: 151974 Hom.: 26882 Cov.: 32 AF XY: 0.593 AC XY: 44030 AN XY: 74272

Gnomad4 AFR AF: 0.638

Gnomad4 AMR AF: 0.529

Gnomad4 ASJ AF: 0.537

Gnomad4 EAS AF: 0.628

Gnomad4 SAS AF: 0.559

Gnomad4 FIN AF: 0.619

Gnomad4 NFE AF: 0.582

Gnomad4 OTH AF: 0.540

Alfa AF: 0.565 Hom.: 9881

Bravo AF: 0.586

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.0
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7765374; hg19: chr6-86944599;