6-92962125-G-C

Position:

• chr6-92962125-G-C

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 0.204 in 151,904 control chromosomes in the GnomAD database, including 5,714 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 0.20 (5714 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.53

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.92962125G>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.204 AC: 30980 AN: 151786 Hom.: 5712 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.0626

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.0544

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.0586

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.204 AC: 31019 AN: 151904 Hom.: 5714 Cov.: 32 AF XY: 0.209 AC XY: 15550 AN XY: 74230

Gnomad4 AFR AF: 0.399

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.758

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.0544

Gnomad4 NFE AF: 0.0586

Gnomad4 OTH AF: 0.202

Alfa AF: 0.0495 Hom.: 69

Bravo AF: 0.231

Asia WGS AF: 0.470 AC: 1629 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.032
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2485846; hg19: chr6-93671843;