6-99814499-C-T

Variant names:

• chr6-99814499-C-T
• rs6916883

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.382 AC: 15818 AN: 41446

American (AMR) AF: 0.536 AC: 8202 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.422 AC: 1464 AN: 3468

East Asian (EAS) AF: 0.970 AC: 5020 AN: 5174

South Asian (SAS) AF: 0.586 AC: 2821 AN: 4810

European-Finnish (FIN) AF: 0.423 AC: 4457 AN: 10540

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.428 AC: 29126 AN: 67992

Other (OTH) AF: 0.438 AC: 924 AN: 2108

Alfa AF: 0.443 Hom.: 8700

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
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs6916883; hg19: chr6-100262375;