11-126158822-T-C

Variant names:

• chr11-126158822-T-C
• rs563519
• ENST00000847743.1:n.14A>G

Variant summary

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

The ENST00000847743.1(ENSG00000287666):​n.14A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 151,768 control chromosomes in the GnomAD database, including 14,544 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 0.39 (14544 hom., cov: 31)
• Consequence: ENSG00000287666 ENST00000847743.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.756
• Publications: 16 publications found

Genes affected

ENSG00000287666 (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 (AFR) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000847743.1. 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
	ENSG00000287666	ENST00000847743.1		n.14A>G		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000287666	ENST00000847740.1		n.-4A>G		upstream_gene	N/A
	ENSG00000287666	ENST00000847741.1		n.-32A>G		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58876 AN: 151650 Hom.: 14519 Cov.: 31

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.388 AC: 58949 AN: 151768 Hom.: 14544 Cov.: 31 AF XY: 0.396 AC XY: 29345 AN XY: 74142

African (AFR) AF: 0.669 AC: 27665 AN: 41370

American (AMR) AF: 0.362 AC: 5519 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1033 AN: 3462

East Asian (EAS) AF: 0.654 AC: 3368 AN: 5150

South Asian (SAS) AF: 0.478 AC: 2296 AN: 4808

European-Finnish (FIN) AF: 0.290 AC: 3046 AN: 10516

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.221 AC: 14982 AN: 67900

Other (OTH) AF: 0.375 AC: 793 AN: 2112

Alfa AF: 0.283 Hom.: 24899

Bravo AF: 0.403

Asia WGS AF: 0.534 AC: 1855 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	1.9
DANN	Benign	0.43
PhyloP100		-0.76

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: rs563519;

hg19: chr11-126028717;