11-36852015-T-C

Variant names:

• chr11-36852015-T-C
• rs7104698
• ENST00000817320.1:n.285-12823T>C

Variant summary

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

The ENST00000817320.1(ENSG00000306379):​n.285-12823T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.725 in 151,940 control chromosomes in the GnomAD database, including 42,742 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 0.73 (42742 hom., cov: 31)
• Consequence: ENSG00000306379 ENST00000817320.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880
• Publications: 7 publications found

Genes affected

ENSG00000306379 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000817320.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306379	ENST00000817320.1		n.285-12823T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.726 AC: 110176 AN: 151822 Hom.: 42742 Cov.: 31

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.726

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.702

Gnomad SAS AF: 0.822

Gnomad FIN AF: 0.924

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.859

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.725 AC: 110208 AN: 151940 Hom.: 42742 Cov.: 31 AF XY: 0.729 AC XY: 54129 AN XY: 74230

African (AFR) AF: 0.432 AC: 17880 AN: 41394

American (AMR) AF: 0.725 AC: 11059 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.869 AC: 3014 AN: 3468

East Asian (EAS) AF: 0.702 AC: 3603 AN: 5134

South Asian (SAS) AF: 0.823 AC: 3959 AN: 4810

European-Finnish (FIN) AF: 0.924 AC: 9800 AN: 10608

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.859 AC: 58359 AN: 67968

Other (OTH) AF: 0.763 AC: 1609 AN: 2110

Alfa AF: 0.819 Hom.: 214450

Bravo AF: 0.699

Asia WGS AF: 0.747 AC: 2597 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.5
DANN	Benign	0.53
PhyloP100		0.088

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7104698;

hg19: chr11-36873565;