11-106242128-T-A

Variant names:

• chr11-106242128-T-A
• rs7111720
• ENST00000657948.1:n.545A>T

Variant summary

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

The ENST00000657948.1(ENSG00000286345):​n.545A>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 0.11 in 152,040 control chromosomes in the GnomAD database, including 1,115 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 0.11 (1115 hom., cov: 31)
• Consequence: ENSG00000286345 ENST00000657948.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.426
• Publications: 0 publications found

Genes affected

ENSG00000286345 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000657948.1. 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
	ENSG00000286345	ENST00000657948.1		n.545A>T		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16690 AN: 151922 Hom.: 1102 Cov.: 31

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.0560

Gnomad AMR AF: 0.0851

Gnomad ASJ AF: 0.0859

Gnomad EAS AF: 0.00890

Gnomad SAS AF: 0.0962

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0772

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.110 AC: 16744 AN: 152040 Hom.: 1115 Cov.: 31 AF XY: 0.112 AC XY: 8307 AN XY: 74308

African (AFR) AF: 0.188 AC: 7775 AN: 41464

American (AMR) AF: 0.0850 AC: 1297 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0859 AC: 298 AN: 3470

East Asian (EAS) AF: 0.00892 AC: 46 AN: 5156

South Asian (SAS) AF: 0.0967 AC: 466 AN: 4818

European-Finnish (FIN) AF: 0.123 AC: 1302 AN: 10560

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.0772 AC: 5248 AN: 68002

Other (OTH) AF: 0.103 AC: 218 AN: 2108

Alfa AF: 0.0958 Hom.: 78

Bravo AF: 0.111

Asia WGS AF: 0.0680 AC: 238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.72
PhyloP100		-0.43

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: rs7111720;

hg19: chr11-106112855;