rs6999813

Variant names:

• chr8-20005960-T-A
• rs6999813

Your query was ambiguous. Multiple possible variants found:

• chr8-20005960-T-A
• chr8-20005960-T-C

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 0.0876 in 152,254 control chromosomes in the GnomAD database, including 593 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 0.088 (593 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.101 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: 0.0877 AC: 13343 AN: 152136 Hom.: 594 Cov.: 33

Gnomad AFR AF: 0.0615

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.0773

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0912

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0862

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

GnomAD4 genome AF: 0.0876 AC: 13333 AN: 152254 Hom.: 593 Cov.: 33 AF XY: 0.0868 AC XY: 6462 AN XY: 74442

African (AFR) AF: 0.0614 AC: 2549 AN: 41546

American (AMR) AF: 0.0772 AC: 1181 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 361 AN: 3470

East Asian (EAS) AF: 0.108 AC: 561 AN: 5184

South Asian (SAS) AF: 0.100 AC: 485 AN: 4826

European-Finnish (FIN) AF: 0.0912 AC: 967 AN: 10600

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6880 AN: 68018

Other (OTH) AF: 0.0853 AC: 180 AN: 2110

Alfa AF: 0.0203 Hom.: 10

Bravo AF: 0.0844

Asia WGS AF: 0.102 AC: 355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.85
DANN	Benign	0.35
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs6999813; hg19: chr8-19863471;