6-99814499-C-T

Position:

• chr6-99814499-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 0.45 in 152,036 control chromosomes in the GnomAD database, including 16,474 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 0.45 (16474 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.948 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: 0.450 AC: 68314 AN: 151918 Hom.: 16463 Cov.: 32

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.970

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.450 AC: 68354 AN: 152036 Hom.: 16474 Cov.: 32 AF XY: 0.457 AC XY: 33960 AN XY: 74304

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.422

Gnomad4 EAS AF: 0.970

Gnomad4 SAS AF: 0.586

Gnomad4 FIN AF: 0.423

Gnomad4 NFE AF: 0.428

Gnomad4 OTH AF: 0.438

Alfa AF: 0.444 Hom.: 5485

Bravo AF: 0.456

Asia WGS AF: 0.749 AC: 2604 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.1
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6916883; hg19: chr6-100262375;