rs934460

Variant names:

• chr11-5513952-A-C
• rs934460
• ENST00000380259.7:n.*739+76873T>G

Your query was ambiguous. Multiple possible variants found:

• chr11-5513952-A-C
• chr11-5513952-A-T

Variant summary

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

The ENST00000380259.7(ENSG00000239920):​n.*739+76873T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 152,094 control chromosomes in the GnomAD database, including 19,324 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 0.50 (19324 hom., cov: 33)
• Consequence: ENSG00000239920 ENST00000380259.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0230

Genes affected

ENSG00000239920 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.639 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
ENSG00000239920	ENST00000380259.7	n.*739+76873T>G		intron_variant	Intron 5 of 7	5		ENSP00000369609.3

Frequencies

GnomAD3 genomes AF: 0.500 AC: 75997 AN: 151976 Hom.: 19307 Cov.: 33

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.500 AC: 76053 AN: 152094 Hom.: 19324 Cov.: 33 AF XY: 0.508 AC XY: 37737 AN XY: 74350

Gnomad4 AFR AF: 0.461

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.465

Gnomad4 EAS AF: 0.658

Gnomad4 SAS AF: 0.635

Gnomad4 FIN AF: 0.564

Gnomad4 NFE AF: 0.481

Gnomad4 OTH AF: 0.504

Alfa AF: 0.340 Hom.: 849

Bravo AF: 0.492

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.64

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs934460; hg19: chr11-5535182;