rs11918092

chr3-134794514-C-Achr3-134794514-C-Gchr3-134794514-C-T

Variant summary

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

The ENST00000656103.1(ENSG00000286982):n.82+1898G>T 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 0.742 in 152,122 control chromosomes in the GnomAD database, including 45,171 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 0.74 (45171 hom., cov: 33)
• Consequence: ENST00000656103.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.262

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.882 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
	ENST00000656103.1	n.82+1898G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.742 AC: 112821 AN: 152004 Hom.: 45180 Cov.: 33

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.817

Gnomad ASJ AF: 0.853

Gnomad EAS AF: 0.902

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.908

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.888

Gnomad OTH AF: 0.791

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

GnomAD4 genome AF: 0.742 AC: 112835 AN: 152122 Hom.: 45171 Cov.: 33 AF XY: 0.742 AC XY: 55204 AN XY: 74394

Gnomad4 AFR AF: 0.415

Gnomad4 AMR AF: 0.817

Gnomad4 ASJ AF: 0.853

Gnomad4 EAS AF: 0.901

Gnomad4 SAS AF: 0.600

Gnomad4 FIN AF: 0.908

Gnomad4 NFE AF: 0.888

Gnomad4 OTH AF: 0.791

Alfa AF: 0.848 Hom.: 54874

Bravo AF: 0.724

Asia WGS AF: 0.709 AC: 2467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	3.5
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11918092; hg19: chr3-134513356;