11-112138255-C-T

Variant names:

• chr11-112138255-C-T
• rs543810
• ENST00000532699.1:n.315-32164C>T

Variant summary

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

The ENST00000532699.1(ENSG00000255292):​n.315-32164C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.829 in 151,922 control chromosomes in the GnomAD database, including 52,738 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 0.83 (52738 hom., cov: 30)
• Consequence: ENSG00000255292 ENST00000532699.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128
• Publications: 11 publications found

Genes affected

ENSG00000255292 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.88 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000532699.1. 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
	ENSG00000255292	ENST00000532699.1	TSL:3	n.315-32164C>T		intron	N/A	ENSP00000456434.1	H3BRW5
	ENSG00000255292	ENST00000525987.5	TSL:4	n.320-32164C>T		intron	N/A
	ENSG00000255292	ENST00000531744.5	TSL:2	n.315-32164C>T		intron	N/A	ENSP00000456957.1	H3BRW5

Frequencies

GnomAD3 genomes AF: 0.830 AC: 125933 AN: 151804 Hom.: 52717 Cov.: 30

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.853

Gnomad AMR AF: 0.843

Gnomad ASJ AF: 0.794

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.902

Gnomad FIN AF: 0.831

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.886

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.829 AC: 126006 AN: 151922 Hom.: 52738 Cov.: 30 AF XY: 0.827 AC XY: 61367 AN XY: 74224

African (AFR) AF: 0.752 AC: 31104 AN: 41376

American (AMR) AF: 0.843 AC: 12851 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.794 AC: 2757 AN: 3472

East Asian (EAS) AF: 0.608 AC: 3140 AN: 5168

South Asian (SAS) AF: 0.903 AC: 4349 AN: 4818

European-Finnish (FIN) AF: 0.831 AC: 8753 AN: 10532

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.886 AC: 60266 AN: 68008

Other (OTH) AF: 0.836 AC: 1760 AN: 2106

Alfa AF: 0.861 Hom.: 71580

Bravo AF: 0.824

Asia WGS AF: 0.790 AC: 2750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.74
PhyloP100		-0.13

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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: rs543810;

hg19: chr11-112008978;