rs836466

Variant names:

• chr11-34715819-G-T
• rs836466
• ENST00000843058.1:n.1562G>T

Variant summary

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

The ENST00000843058.1(ENSG00000309692):​n.1562G>T 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 0.511 in 151,946 control chromosomes in the GnomAD database, including 20,615 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 0.51 (20615 hom., cov: 32)
• Consequence: ENSG00000309692 ENST00000843058.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.169
• Publications: 3 publications found

Genes affected

ENSG00000309692 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000843058.1. 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
	ENSG00000309692	ENST00000843058.1		n.1562G>T		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000309692	ENST00000843048.1		n.506+22930G>T		intron	N/A
	ENSG00000309692	ENST00000843049.1		n.698+13804G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77657 AN: 151828 Hom.: 20590 Cov.: 32

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.511 AC: 77720 AN: 151946 Hom.: 20615 Cov.: 32 AF XY: 0.502 AC XY: 37305 AN XY: 74246

African (AFR) AF: 0.571 AC: 23652 AN: 41426

American (AMR) AF: 0.384 AC: 5854 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.549 AC: 1902 AN: 3466

East Asian (EAS) AF: 0.131 AC: 678 AN: 5172

South Asian (SAS) AF: 0.428 AC: 2064 AN: 4820

European-Finnish (FIN) AF: 0.467 AC: 4930 AN: 10554

Middle Eastern (MID) AF: 0.476 AC: 139 AN: 292

European-Non Finnish (NFE) AF: 0.540 AC: 36722 AN: 67956

Other (OTH) AF: 0.517 AC: 1088 AN: 2104

Alfa AF: 0.535 Hom.: 2868

Bravo AF: 0.503

Asia WGS AF: 0.245 AC: 853 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.52
PhyloP100		-0.17

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: rs836466;

hg19: chr11-34737366;