11-116736721-C-T

Variant names:

• chr11-116736721-C-T
• rs1558861
• ENST00000836679.1:n.339-1699C>T

Variant summary

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

The ENST00000836679.1(ENSG00000308823):​n.339-1699C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.927 in 152,246 control chromosomes in the GnomAD database, including 65,754 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 0.93 (65754 hom., cov: 31)
• Consequence: ENSG00000308823 ENST00000836679.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 43 publications found

Genes affected

ENSG00000308823 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.976 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
ENSG00000308823	ENST00000836679.1	n.339-1699C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.928 AC: 141104 AN: 152128 Hom.: 65706 Cov.: 31

Gnomad AFR AF: 0.984

Gnomad AMI AF: 0.897

Gnomad AMR AF: 0.876

Gnomad ASJ AF: 0.906

Gnomad EAS AF: 0.767

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.919

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.929

Gnomad OTH AF: 0.922

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

GnomAD4 genome AF: 0.927 AC: 141208 AN: 152246 Hom.: 65754 Cov.: 31 AF XY: 0.923 AC XY: 68717 AN XY: 74432

African (AFR) AF: 0.984 AC: 40892 AN: 41550

American (AMR) AF: 0.876 AC: 13390 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.906 AC: 3143 AN: 3470

East Asian (EAS) AF: 0.766 AC: 3971 AN: 5184

South Asian (SAS) AF: 0.805 AC: 3874 AN: 4814

European-Finnish (FIN) AF: 0.919 AC: 9739 AN: 10598

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.929 AC: 63177 AN: 68018

Other (OTH) AF: 0.918 AC: 1942 AN: 2116

Alfa AF: 0.930 Hom.: 48477

Bravo AF: 0.927

Asia WGS AF: 0.799 AC: 2782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.73
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1558861; hg19: chr11-116607437;