rs7933007

Variant names:

• chr11-118859960-C-T
• rs7933007
• ENST00000816613.1:n.124+7215G>A

Variant summary

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

The ENST00000816613.1(ENSG00000306274):​n.124+7215G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.783 in 152,028 control chromosomes in the GnomAD database, including 46,903 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 0.78 (46903 hom., cov: 30)
• Consequence: ENSG00000306274 ENST00000816613.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.652
• Publications: 9 publications found

Genes affected

ENSG00000306274 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.84 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
ENSG00000306274	ENST00000816613.1	n.124+7215G>A		intron_variant	Intron 2 of 2
ENSG00000306274	ENST00000816614.1	n.272+7215G>A		intron_variant	Intron 2 of 2
ENSG00000306274	ENST00000816615.1	n.251+10409G>A		intron_variant	Intron 1 of 1
ENSG00000306274	ENST00000816616.1	n.244+10409G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.783 AC: 118979 AN: 151912 Hom.: 46842 Cov.: 30

Gnomad AFR AF: 0.847

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.848

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.794

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

GnomAD4 genome AF: 0.783 AC: 119100 AN: 152028 Hom.: 46903 Cov.: 30 AF XY: 0.779 AC XY: 57863 AN XY: 74316

African (AFR) AF: 0.847 AC: 35142 AN: 41472

American (AMR) AF: 0.848 AC: 12953 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.814 AC: 2827 AN: 3472

East Asian (EAS) AF: 0.717 AC: 3713 AN: 5182

South Asian (SAS) AF: 0.549 AC: 2638 AN: 4806

European-Finnish (FIN) AF: 0.724 AC: 7629 AN: 10538

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.759 AC: 51575 AN: 67976

Other (OTH) AF: 0.791 AC: 1670 AN: 2110

Alfa AF: 0.762 Hom.: 34400

Bravo AF: 0.801

Asia WGS AF: 0.661 AC: 2299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.81
DANN	Benign	0.46
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs7933007; hg19: chr11-118730669;