rs7999876

Variant names:

• chr13-86018689-G-A
• rs7999876

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 0.0798 in 151,750 control chromosomes in the GnomAD database, including 1,000 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 0.080 (1000 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.481
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 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: 0.0797 AC: 12088 AN: 151632 Hom.: 1001 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0459

Gnomad ASJ AF: 0.0176

Gnomad EAS AF: 0.0431

Gnomad SAS AF: 0.0839

Gnomad FIN AF: 0.0417

Gnomad MID AF: 0.0191

Gnomad NFE AF: 0.0195

Gnomad OTH AF: 0.0590

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

GnomAD4 genome AF: 0.0798 AC: 12114 AN: 151750 Hom.: 1000 Cov.: 32 AF XY: 0.0808 AC XY: 5990 AN XY: 74148

African (AFR) AF: 0.213 AC: 8803 AN: 41378

American (AMR) AF: 0.0458 AC: 698 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.0176 AC: 61 AN: 3464

East Asian (EAS) AF: 0.0432 AC: 223 AN: 5162

South Asian (SAS) AF: 0.0841 AC: 405 AN: 4814

European-Finnish (FIN) AF: 0.0417 AC: 437 AN: 10480

Middle Eastern (MID) AF: 0.0205 AC: 6 AN: 292

European-Non Finnish (NFE) AF: 0.0195 AC: 1325 AN: 67892

Other (OTH) AF: 0.0612 AC: 129 AN: 2108

Alfa AF: 0.0572 Hom.: 101

Bravo AF: 0.0854

Asia WGS AF: 0.0790 AC: 276 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.1
DANN	Benign	0.62
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs7999876; hg19: chr13-86592824;