ENST00000451108.2:n.111+1293A>G

Variant names:

• chr9-110600821-A-G
• rs4978941
• ENST00000451108.2:n.111+1293A>G

Variant summary

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

The ENST00000451108.2(ENSG00000232896):​n.111+1293A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 151,694 control chromosomes in the GnomAD database, including 9,275 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 0.33 (9275 hom., cov: 31)
• Consequence: ENSG00000232896 ENST00000451108.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.493
• Publications: 2 publications found

Genes affected

ENSG00000232896 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000451108.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000232896	ENST00000451108.2	TSL:3	n.111+1293A>G		intron	N/A
	ENSG00000232896	ENST00000828035.1		n.111+1293A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50523 AN: 151576 Hom.: 9259 Cov.: 31

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.333 AC: 50575 AN: 151694 Hom.: 9275 Cov.: 31 AF XY: 0.341 AC XY: 25266 AN XY: 74120

African (AFR) AF: 0.215 AC: 8898 AN: 41364

American (AMR) AF: 0.499 AC: 7596 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1181 AN: 3472

East Asian (EAS) AF: 0.562 AC: 2896 AN: 5150

South Asian (SAS) AF: 0.396 AC: 1907 AN: 4820

European-Finnish (FIN) AF: 0.408 AC: 4252 AN: 10416

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.337 AC: 22866 AN: 67944

Other (OTH) AF: 0.350 AC: 737 AN: 2104

Alfa AF: 0.330 Hom.: 1359

Bravo AF: 0.338

Asia WGS AF: 0.461 AC: 1597 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.0
DANN	Benign	0.47
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs4978941; hg19: chr9-113363101;