rs11098092

chr4-110877045-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000681682.1(ENSG00000288692):n.433+203G>A variant causes a intron, non coding transcript 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: ENST00000681682.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000681682.1	n.433+203G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.502

Gnomad4 ASJ AF: 0.578

Gnomad4 EAS AF: 0.438

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.559

Gnomad4 OTH AF: 0.498

Alfa AF: 0.544 Hom.: 45804

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11098092; hg19: chr4-111798201;