ENST00000671134.1:n.324-41950T>A

Variant names:

• chr11-81232926-T-A
• rs4943819
• ENST00000671134.1:n.324-41950T>A

Variant summary

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

The ENST00000671134.1(ENSG00000287912):​n.324-41950T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 151,514 control chromosomes in the GnomAD database, including 23,198 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 0.53 (23198 hom., cov: 32)
• Consequence: ENSG00000287912 ENST00000671134.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.431

Genes affected

ENSG00000287912 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.915 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.324-41950T>A		intron_variant	Intron 2 of 4
ENSG00000287912	ENST00000671210.1	n.310-41950T>A		intron_variant	Intron 2 of 2
ENSG00000287912	ENST00000701193.1	n.114-41950T>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79540 AN: 151396 Hom.: 23141 Cov.: 32

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.526 AC: 79654 AN: 151514 Hom.: 23198 Cov.: 32 AF XY: 0.527 AC XY: 38975 AN XY: 74024

Gnomad4 AFR AF: 0.734

Gnomad4 AMR AF: 0.586

Gnomad4 ASJ AF: 0.447

Gnomad4 EAS AF: 0.937

Gnomad4 SAS AF: 0.476

Gnomad4 FIN AF: 0.356

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.546

Alfa AF: 0.470 Hom.: 2273

Bravo AF: 0.556

Asia WGS AF: 0.739 AC: 2554 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.1
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4943819; hg19: chr11-80943969;