rs11098092

Variant names:

• chr4-110877045-G-A
• rs11098092
• ENST00000719652.1:n.341G>A

Variant summary

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

The ENST00000719652.1(ENSG00000288692):​n.341G>A 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 0.491 in 151,796 control chromosomes in the GnomAD database, including 18,911 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 0.49 (18911 hom., cov: 31)
• Consequence: ENSG00000288692 ENST00000719652.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• Publications: 9 publications found

Genes affected

ENSG00000288692 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288692	ENST00000719652.1	n.341G>A		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000288692	ENST00000681682.2	n.433+203G>A		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74514 AN: 151678 Hom.: 18906 Cov.: 31

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.491 AC: 74530 AN: 151796 Hom.: 18911 Cov.: 31 AF XY: 0.490 AC XY: 36300 AN XY: 74152

African (AFR) AF: 0.369 AC: 15273 AN: 41392

American (AMR) AF: 0.502 AC: 7649 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2004 AN: 3466

East Asian (EAS) AF: 0.438 AC: 2259 AN: 5152

South Asian (SAS) AF: 0.454 AC: 2180 AN: 4806

European-Finnish (FIN) AF: 0.516 AC: 5414 AN: 10498

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.559 AC: 37957 AN: 67914

Other (OTH) AF: 0.498 AC: 1052 AN: 2114

Alfa AF: 0.532 Hom.: 71658

Bravo AF: 0.484

Asia WGS AF: 0.420 AC: 1458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.0
DANN	Benign	0.62
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs11098092; hg19: chr4-111798201;