chr11-112172891-G-A

Variant names:

• chr11-112172891-G-A
• rs11214108
• ENST00000532699.1:n.*55+2217G>A

Variant summary

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

The ENST00000532699.1(ENSG00000255292):​n.*55+2217G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,056 control chromosomes in the GnomAD database, including 1,355 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 0.12 (1355 hom., cov: 32)
• Consequence: ENSG00000255292 ENST00000532699.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.610
• Publications: 9 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.376 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.*55+2217G>A		intron	N/A	ENSP00000456434.1	H3BRW5
	ENSG00000255292	ENST00000525987.5	TSL:4	n.431+2361G>A		intron	N/A
	ENSG00000255292	ENST00000531744.5	TSL:2	n.*55+2217G>A		intron	N/A	ENSP00000456957.1	H3BRW5

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17888 AN: 151938 Hom.: 1356 Cov.: 32

Gnomad AFR AF: 0.0702

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.0545

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.118 AC: 17907 AN: 152056 Hom.: 1355 Cov.: 32 AF XY: 0.121 AC XY: 9010 AN XY: 74308

African (AFR) AF: 0.0705 AC: 2923 AN: 41482

American (AMR) AF: 0.138 AC: 2114 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 646 AN: 3468

East Asian (EAS) AF: 0.391 AC: 2017 AN: 5164

South Asian (SAS) AF: 0.0545 AC: 263 AN: 4822

European-Finnish (FIN) AF: 0.158 AC: 1666 AN: 10554

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.115 AC: 7831 AN: 67974

Other (OTH) AF: 0.132 AC: 278 AN: 2106

Alfa AF: 0.119 Hom.: 1659

Bravo AF: 0.117

Asia WGS AF: 0.177 AC: 613 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.3
DANN	Benign	0.28
PhyloP100		0.61

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

Other links and lift over

dbSNP: rs11214108; hg19: chr11-112043614;