rs11887092

Variant names:

• chr2-188972572-A-G
• rs11887092
• ENST00000803235.1:n.103+12139T>C

Variant summary

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

The ENST00000803235.1(ENSG00000304419):​n.103+12139T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0767 in 152,124 control chromosomes in the GnomAD database, including 1,149 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 0.077 (1149 hom., cov: 32)
• Consequence: ENSG00000304419 ENST00000803235.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490
• Publications: 4 publications found

Genes affected

ENSG00000304419 (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 (AFR) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373791	XR_007087614.1	n.110-2093T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304419	ENST00000803235.1	n.103+12139T>C		intron_variant	Intron 1 of 1
ENSG00000304419	ENST00000803236.1	n.325-2093T>C		intron_variant	Intron 2 of 3
ENSG00000304419	ENST00000803237.1	n.191-5906T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0765 AC: 11623 AN: 152006 Hom.: 1141 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0848

Gnomad ASJ AF: 0.00346

Gnomad EAS AF: 0.0998

Gnomad SAS AF: 0.0343

Gnomad FIN AF: 0.00906

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.00318

Gnomad OTH AF: 0.0664

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

GnomAD4 genome AF: 0.0767 AC: 11671 AN: 152124 Hom.: 1149 Cov.: 32 AF XY: 0.0757 AC XY: 5631 AN XY: 74378

African (AFR) AF: 0.222 AC: 9204 AN: 41476

American (AMR) AF: 0.0852 AC: 1302 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.00346 AC: 12 AN: 3468

East Asian (EAS) AF: 0.0998 AC: 515 AN: 5160

South Asian (SAS) AF: 0.0346 AC: 167 AN: 4830

European-Finnish (FIN) AF: 0.00906 AC: 96 AN: 10592

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.00318 AC: 216 AN: 67996

Other (OTH) AF: 0.0672 AC: 142 AN: 2114

Alfa AF: 0.0447 Hom.: 804

Bravo AF: 0.0914

Asia WGS AF: 0.0830 AC: 286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.9
DANN	Benign	0.53
PhyloP100		-0.049

Splicing

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

Other links and lift over

dbSNP: rs11887092; hg19: chr2-189837298;