chr11-106603534-A-G

Variant names:

• chr11-106603534-A-G
• rs11821466
• ENST00000692272.2:n.313+639T>C

Variant summary

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

The ENST00000692272.2(ENSG00000289232):​n.313+639T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 151,914 control chromosomes in the GnomAD database, including 11,736 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 0.35 (11736 hom., cov: 32)
• Consequence: ENSG00000289232 ENST00000692272.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 0 publications found

Genes affected

ENSG00000289232 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000692272.2. 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
	ENSG00000289232	ENST00000692272.2		n.313+639T>C		intron	N/A
	ENSG00000289232	ENST00000728091.1		n.219+639T>C		intron	N/A
	ENSG00000289232	ENST00000728092.1		n.230+639T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52658 AN: 151796 Hom.: 11695 Cov.: 32

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.0390

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.347 AC: 52762 AN: 151914 Hom.: 11736 Cov.: 32 AF XY: 0.345 AC XY: 25602 AN XY: 74240

African (AFR) AF: 0.631 AC: 26128 AN: 41412

American (AMR) AF: 0.266 AC: 4048 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 480 AN: 3466

East Asian (EAS) AF: 0.0388 AC: 201 AN: 5174

South Asian (SAS) AF: 0.137 AC: 661 AN: 4824

European-Finnish (FIN) AF: 0.349 AC: 3678 AN: 10532

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16647 AN: 67954

Other (OTH) AF: 0.317 AC: 666 AN: 2102

Alfa AF: 0.218 Hom.: 1617

Bravo AF: 0.356

Asia WGS AF: 0.124 AC: 432 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.068
DANN	Benign	0.39
PhyloP100		-1.1

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: rs11821466;

hg19: chr11-106474261;