6-93826906-T-C

Position:

• chr6-93826906-T-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 0.583 in 151,798 control chromosomes in the GnomAD database, including 26,274 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 0.58 (26274 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.201

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.93826906T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88406 AN: 151682 Hom.: 26246 Cov.: 32

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.583 AC: 88497 AN: 151798 Hom.: 26274 Cov.: 32 AF XY: 0.584 AC XY: 43320 AN XY: 74190

Gnomad4 AFR AF: 0.678

Gnomad4 AMR AF: 0.525

Gnomad4 ASJ AF: 0.508

Gnomad4 EAS AF: 0.573

Gnomad4 SAS AF: 0.679

Gnomad4 FIN AF: 0.517

Gnomad4 NFE AF: 0.552

Gnomad4 OTH AF: 0.538

Alfa AF: 0.551 Hom.: 7293

Bravo AF: 0.577

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6941459; hg19: chr6-94536624; COSMIC: COSV64445482;