6-92640045-C-T

Position:

• chr6-92640045-C-T

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 0.853 in 152,102 control chromosomes in the GnomAD database, including 56,351 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 0.85 (56351 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.939 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: 0.854 AC: 129742 AN: 151982 Hom.: 56336 Cov.: 32

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.834

Gnomad ASJ AF: 0.929

Gnomad EAS AF: 0.716

Gnomad SAS AF: 0.912

Gnomad FIN AF: 0.913

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.945

Gnomad OTH AF: 0.868

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

GnomAD4 genome AF: 0.853 AC: 129802 AN: 152102 Hom.: 56351 Cov.: 32 AF XY: 0.851 AC XY: 63277 AN XY: 74346

Gnomad4 AFR AF: 0.696

Gnomad4 AMR AF: 0.835

Gnomad4 ASJ AF: 0.929

Gnomad4 EAS AF: 0.716

Gnomad4 SAS AF: 0.912

Gnomad4 FIN AF: 0.913

Gnomad4 NFE AF: 0.945

Gnomad4 OTH AF: 0.865

Alfa AF: 0.926 Hom.: 128154

Bravo AF: 0.838

Asia WGS AF: 0.796 AC: 2768 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1841258; hg19: chr6-93349763;