chr6-92810539-C-A

Position:

• chr6-92810539-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 0.389 in 151,982 control chromosomes in the GnomAD database, including 12,319 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 0.39 (12319 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.570

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.546 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: 0.388 AC: 58988 AN: 151866 Hom.: 12294 Cov.: 32

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.389 AC: 59058 AN: 151982 Hom.: 12319 Cov.: 32 AF XY: 0.384 AC XY: 28508 AN XY: 74264

Gnomad4 AFR AF: 0.552

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.377

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.396

Alfa AF: 0.353 Hom.: 14407

Bravo AF: 0.392

Asia WGS AF: 0.279 AC: 965 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	10
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9294536; hg19: chr6-93520257;