rs7999069

Variant names:

• chr13-21812351-A-G
• rs7999069
• ENST00000785194.1:n.221-1207A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000785194.1(ENSG00000302249):​n.221-1207A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.547 in 152,124 control chromosomes in the GnomAD database, including 23,525 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 0.55 (23525 hom., cov: 33)
• Consequence: ENSG00000302249 ENST00000785194.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.78
• Publications: 2 publications found

Genes affected

ENSG00000302249 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903132	XR_007063714.1	n.216-1207A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302249	ENST00000785194.1	n.221-1207A>G		intron_variant	Intron 1 of 2
ENSG00000302249	ENST00000785195.1	n.236-1207A>G		intron_variant	Intron 1 of 2
ENSG00000302249	ENST00000785196.1	n.239-1207A>G		intron_variant	Intron 1 of 1
ENSG00000302249	ENST00000785197.1	n.-151A>G		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.547 AC: 83132 AN: 152006 Hom.: 23523 Cov.: 33

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.547 AC: 83170 AN: 152124 Hom.: 23525 Cov.: 33 AF XY: 0.546 AC XY: 40584 AN XY: 74368

African (AFR) AF: 0.406 AC: 16861 AN: 41510

American (AMR) AF: 0.623 AC: 9520 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.626 AC: 2171 AN: 3468

East Asian (EAS) AF: 0.466 AC: 2402 AN: 5154

South Asian (SAS) AF: 0.413 AC: 1992 AN: 4820

European-Finnish (FIN) AF: 0.609 AC: 6458 AN: 10598

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.615 AC: 41788 AN: 67966

Other (OTH) AF: 0.567 AC: 1197 AN: 2112

Alfa AF: 0.590 Hom.: 54549

Bravo AF: 0.541

Asia WGS AF: 0.443 AC: 1538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	15
DANN	Benign	0.69
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs7999069; hg19: chr13-22386490;