chr11-112135216-A-G

Variant names:

• chr11-112135216-A-G
• rs243908
• ENST00000532699.1:n.315-35203A>G

Variant summary

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

The ENST00000532699.1(ENSG00000255292):​n.315-35203A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 151,998 control chromosomes in the GnomAD database, including 6,138 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 0.28 (6138 hom., cov: 30)
• Consequence: ENSG00000255292 ENST00000532699.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.67
• Publications: 26 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.319 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.315-35203A>G		intron	N/A	ENSP00000456434.1	H3BRW5
	ENSG00000255292	ENST00000525987.5	TSL:4	n.320-35203A>G		intron	N/A
	ENSG00000255292	ENST00000531744.5	TSL:2	n.315-35203A>G		intron	N/A	ENSP00000456957.1	H3BRW5

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42352 AN: 151880 Hom.: 6140 Cov.: 30

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.279 AC: 42341 AN: 151998 Hom.: 6138 Cov.: 30 AF XY: 0.279 AC XY: 20703 AN XY: 74288

African (AFR) AF: 0.219 AC: 9096 AN: 41458

American (AMR) AF: 0.326 AC: 4979 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1017 AN: 3468

East Asian (EAS) AF: 0.143 AC: 739 AN: 5154

South Asian (SAS) AF: 0.232 AC: 1118 AN: 4824

European-Finnish (FIN) AF: 0.323 AC: 3407 AN: 10554

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.311 AC: 21115 AN: 67970

Other (OTH) AF: 0.271 AC: 571 AN: 2106

Alfa AF: 0.294 Hom.: 11565

Bravo AF: 0.278

Asia WGS AF: 0.201 AC: 701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.0
DANN	Benign	0.81
PhyloP100		1.7

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs243908; hg19: chr11-112005939;