rs6999868

Variant names:

• chr8-5657411-G-T
• rs6999868

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 0.145 in 152,190 control chromosomes in the GnomAD database, including 1,720 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 0.14 (1720 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.260

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.169 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: 0.145 AC: 21986 AN: 152072 Hom.: 1717 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.0892

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.145 AC: 21999 AN: 152190 Hom.: 1720 Cov.: 32 AF XY: 0.143 AC XY: 10650 AN XY: 74386

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.0891

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.139

Alfa AF: 0.145 Hom.: 1642

Bravo AF: 0.140

Asia WGS AF: 0.0860 AC: 298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6999868; hg19: chr8-5514933;