rs10790268

Variant names:

• chr11-118858682-A-G
• rs10790268
• ENST00000816613.1:n.124+8493T>C

Your query was ambiguous. Multiple possible variants found:

• chr11-118858682-A-G
• chr11-118858682-A-T

Variant summary

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

The ENST00000816613.1(ENSG00000306274):​n.124+8493T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.802 in 150,956 control chromosomes in the GnomAD database, including 48,613 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 0.80 (48613 hom., cov: 26)
• Consequence: ENSG00000306274 ENST00000816613.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.613
• Publications: 31 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=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.852 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+8493T>C		intron_variant	Intron 2 of 2
ENSG00000306274	ENST00000816614.1	n.272+8493T>C		intron_variant	Intron 2 of 2
ENSG00000306274	ENST00000816615.1	n.251+11687T>C		intron_variant	Intron 1 of 1
ENSG00000306274	ENST00000816616.1	n.245-9734T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.802 AC: 121002 AN: 150838 Hom.: 48558 Cov.: 26

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.828

Gnomad ASJ AF: 0.824

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.839

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.822

Gnomad NFE AF: 0.802

Gnomad OTH AF: 0.816

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

GnomAD4 genome AF: 0.802 AC: 121114 AN: 150956 Hom.: 48613 Cov.: 26 AF XY: 0.804 AC XY: 59272 AN XY: 73678

African (AFR) AF: 0.772 AC: 31761 AN: 41122

American (AMR) AF: 0.828 AC: 12541 AN: 15138

Ashkenazi Jewish (ASJ) AF: 0.824 AC: 2855 AN: 3464

East Asian (EAS) AF: 0.874 AC: 4438 AN: 5080

South Asian (SAS) AF: 0.838 AC: 4004 AN: 4778

European-Finnish (FIN) AF: 0.829 AC: 8540 AN: 10302

Middle Eastern (MID) AF: 0.825 AC: 241 AN: 292

European-Non Finnish (NFE) AF: 0.802 AC: 54344 AN: 67780

Other (OTH) AF: 0.818 AC: 1709 AN: 2090

Alfa AF: 0.738 Hom.: 2200

Bravo AF: 0.804

Asia WGS AF: 0.849 AC: 2948 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.88
DANN	Benign	0.13
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs10790268; hg19: chr11-118729391;