rs1458095

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

Genes affected

ENSG00000287912 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000671134.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287912	ENST00000671134.1		n.324-371C>T		intron	N/A
	ENSG00000287912	ENST00000671210.1		n.310-371C>T		intron	N/A
	ENSG00000287912	ENST00000701193.2		n.196-371C>T		intron	N/A

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

African (AFR) AF: 0.332 AC: 13715 AN: 41352

American (AMR) AF: 0.175 AC: 2669 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0804 AC: 279 AN: 3470

East Asian (EAS) AF: 0.193 AC: 997 AN: 5154

South Asian (SAS) AF: 0.218 AC: 1052 AN: 4816

European-Finnish (FIN) AF: 0.135 AC: 1423 AN: 10558

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0931 AC: 6328 AN: 67996

Other (OTH) AF: 0.149 AC: 313 AN: 2102

Alfa AF: 0.119 Hom.: 6480

Bravo AF: 0.184

Asia WGS AF: 0.206 AC: 713 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.89
DANN	Benign	0.24
PhyloP100		-0.55

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1458095;

hg19: chr11-80985548;