rs1458072

Variant names:

• chr11-81263412-A-G
• rs1458072
• ENST00000671134.1:n.324-11464A>G

Variant summary

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

The ENST00000671134.1(ENSG00000287912):​n.324-11464A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.828 in 151,478 control chromosomes in the GnomAD database, including 51,979 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 0.83 (51979 hom., cov: 32)
• Consequence: ENSG00000287912 ENST00000671134.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.780

Genes affected

ENSG00000287912 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.946 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
ENSG00000287912	ENST00000671134.1	n.324-11464A>G		intron_variant	Intron 2 of 4
ENSG00000287912	ENST00000671210.1	n.310-11464A>G		intron_variant	Intron 2 of 2
ENSG00000287912	ENST00000701193.1	n.114-11464A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.828 AC: 125304 AN: 151360 Hom.: 51943 Cov.: 32

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.871

Gnomad AMR AF: 0.847

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 0.968

Gnomad SAS AF: 0.866

Gnomad FIN AF: 0.831

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.817

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

GnomAD4 genome AF: 0.828 AC: 125394 AN: 151478 Hom.: 51979 Cov.: 32 AF XY: 0.831 AC XY: 61465 AN XY: 74004

Gnomad4 AFR AF: 0.812

Gnomad4 AMR AF: 0.847

Gnomad4 ASJ AF: 0.846

Gnomad4 EAS AF: 0.968

Gnomad4 SAS AF: 0.865

Gnomad4 FIN AF: 0.831

Gnomad4 NFE AF: 0.818

Gnomad4 OTH AF: 0.815

Alfa AF: 0.824 Hom.: 23415

Bravo AF: 0.830

Asia WGS AF: 0.901 AC: 3118 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.53
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1458072; hg19: chr11-80974455;