ENST00000837879.1:n.158+232C>T

Variant names:

• chr11-92218988-G-A
• rs1350445
• ENST00000837879.1:n.158+232C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000837879.1(ENSG00000309025):​n.158+232C>T variant causes a intron change. The variant allele was found at a frequency of 0.787 in 152,100 control chromosomes in the GnomAD database, including 47,291 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 0.79 (47291 hom., cov: 32)
• Consequence: ENSG00000309025 ENST00000837879.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.59
• Publications: 11 publications found

Genes affected

ENSG00000309025 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000837879.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309025	ENST00000837879.1		n.158+232C>T		intron	N/A
	ENSG00000309025	ENST00000837880.1		n.117+232C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.787 AC: 119660 AN: 151982 Hom.: 47247 Cov.: 32

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.866

Gnomad AMR AF: 0.837

Gnomad ASJ AF: 0.802

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.838

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.788

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

GnomAD4 genome AF: 0.787 AC: 119762 AN: 152100 Hom.: 47291 Cov.: 32 AF XY: 0.785 AC XY: 58335 AN XY: 74358

African (AFR) AF: 0.812 AC: 33692 AN: 41506

American (AMR) AF: 0.837 AC: 12791 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.802 AC: 2785 AN: 3472

East Asian (EAS) AF: 0.616 AC: 3174 AN: 5150

South Asian (SAS) AF: 0.839 AC: 4044 AN: 4822

European-Finnish (FIN) AF: 0.707 AC: 7469 AN: 10566

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.781 AC: 53106 AN: 67988

Other (OTH) AF: 0.788 AC: 1662 AN: 2108

Alfa AF: 0.778 Hom.: 66725

Bravo AF: 0.795

Asia WGS AF: 0.741 AC: 2575 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	12
DANN	Benign	0.42
PhyloP100		3.6

Splicing

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

Other links and lift over

dbSNP: rs1350445; hg19: chr11-91952154;