rs7999876

chr13-86018689-G-A

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 0.0798 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.0458

Gnomad4 ASJ AF: 0.0176

Gnomad4 EAS AF: 0.0432

Gnomad4 SAS AF: 0.0841

Gnomad4 FIN AF: 0.0417

Gnomad4 NFE AF: 0.0195

Gnomad4 OTH AF: 0.0612

Alfa AF: 0.0518 Hom.: 85

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7999876; hg19: chr13-86592824;