rs1458095

Variant names:

• chr11-81274505-C-T
• rs1458095
• ENST00000671134.1:n.324-371C>T

Variant summary

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

The ENST00000671134.1(ENSG00000287912):​n.324-371C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 151,914 control chromosomes in the GnomAD database, including 3,258 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 0.18 (3258 hom., cov: 32)
• Consequence: ENSG00000287912 ENST00000671134.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.550

Genes affected

ENSG00000287912 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.327 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.324-371C>T		intron_variant	Intron 2 of 4
ENSG00000287912	ENST00000671210.1	n.310-371C>T		intron_variant	Intron 2 of 2
ENSG00000287912	ENST00000701193.1	n.114-371C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26806 AN: 151796 Hom.: 3254 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.0804

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0931

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.177 AC: 26831 AN: 151914 Hom.: 3258 Cov.: 32 AF XY: 0.180 AC XY: 13372 AN XY: 74252

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.0804

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.0931

Gnomad4 OTH AF: 0.149

Alfa AF: 0.108 Hom.: 2482

Bravo AF: 0.184

Asia WGS AF: 0.206 AC: 713 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.89
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1458095; hg19: chr11-80985548;