6-88584026-A-G

Position:

• chr6-88584026-A-G

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 0.214 in 152,132 control chromosomes in the GnomAD database, including 4,562 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 0.21 (4562 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.435

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.375 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: 0.214 AC: 32548 AN: 152014 Hom.: 4562 Cov.: 32

Gnomad AFR AF: 0.0566

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.0848

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.214 AC: 32548 AN: 152132 Hom.: 4562 Cov.: 32 AF XY: 0.218 AC XY: 16196 AN XY: 74360

Gnomad4 AFR AF: 0.0565

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.287

Gnomad4 EAS AF: 0.0844

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.289

Gnomad4 OTH AF: 0.199

Alfa AF: 0.265 Hom.: 10493

Bravo AF: 0.189

Asia WGS AF: 0.226 AC: 785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.1
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12527253; hg19: chr6-89293745;