11-116741111-A-T

Variant names:

• chr11-116741111-A-T
• rs180349
• ENST00000836679.1:n.433+2597A>T

Variant summary

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

The ENST00000836679.1(ENSG00000308823):​n.433+2597A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 152,012 control chromosomes in the GnomAD database, including 42,387 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 0.74 (42387 hom., cov: 30)
• Consequence: ENSG00000308823 ENST00000836679.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.754
• Publications: 27 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 = 0.826 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.433+2597A>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.744 AC: 113013 AN: 151894 Hom.: 42363 Cov.: 30

Gnomad AFR AF: 0.833

Gnomad AMI AF: 0.635

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.767

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.727

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

GnomAD4 genome AF: 0.744 AC: 113093 AN: 152012 Hom.: 42387 Cov.: 30 AF XY: 0.742 AC XY: 55143 AN XY: 74292

African (AFR) AF: 0.833 AC: 34536 AN: 41464

American (AMR) AF: 0.738 AC: 11274 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.689 AC: 2392 AN: 3472

East Asian (EAS) AF: 0.766 AC: 3947 AN: 5150

South Asian (SAS) AF: 0.700 AC: 3368 AN: 4808

European-Finnish (FIN) AF: 0.693 AC: 7321 AN: 10562

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.705 AC: 47937 AN: 67960

Other (OTH) AF: 0.725 AC: 1530 AN: 2110

Alfa AF: 0.723 Hom.: 4678

Bravo AF: 0.752

Asia WGS AF: 0.741 AC: 2580 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	1.1
DANN	Benign	0.66
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs180349; hg19: chr11-116611827;