6-100891102-T-C

Position:

• chr6-100891102-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 0.514 in 151,856 control chromosomes in the GnomAD database, including 20,430 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 0.51 (20430 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.887

Genes affected

(HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.728 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.100891102T>C		intergenic_region
LOC107984041	XR_002956381.2	n.199-896T>C		intron_variant
LOC107984041	XR_002956382.2	n.199-896T>C		intron_variant
LOC107984041	XR_007059692.1	n.199-896T>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78037 AN: 151738 Hom.: 20401 Cov.: 32

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.747

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.514 AC: 78112 AN: 151856 Hom.: 20430 Cov.: 32 AF XY: 0.513 AC XY: 38107 AN XY: 74226

Gnomad4 AFR AF: 0.451

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.530

Gnomad4 EAS AF: 0.747

Gnomad4 SAS AF: 0.374

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.536

Alfa AF: 0.510 Hom.: 10583

Bravo AF: 0.527

Asia WGS AF: 0.558 AC: 1929 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.9
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6919745; hg19: chr6-101338978;