chr3-134794514-C-A

Variant names:

• chr3-134794514-C-A
• rs11918092
• ENST00000460895.5:n.218+14633C>A

Variant summary

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

The ENST00000460895.5(ENSG00000288700):​n.218+14633C>A variant causes a intron 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: ENSG00000288700 ENST00000460895.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.262

Genes affected

ENSG00000288700 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288700	ENST00000460895.5	n.218+14633C>A		intron_variant	Intron 2 of 3	3
ENSG00000286982	ENST00000656103.1	n.82+1898G>T		intron_variant	Intron 1 of 1

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;