ENST00000750211.1:n.497+45206A>C

Variant names:

• chr9-119719629-T-G
• rs4642724
• ENST00000750211.1:n.497+45206A>C

Variant summary

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

The ENST00000750211.1(ENSG00000297691):​n.497+45206A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.913 in 152,162 control chromosomes in the GnomAD database, including 63,444 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 0.91 (63444 hom., cov: 32)
• Consequence: ENSG00000297691 ENST00000750211.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.932
• Publications: 3 publications found

Genes affected

ENSG00000297691 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.956 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000750211.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297691	ENST00000750211.1		n.497+45206A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.913 AC: 138783 AN: 152044 Hom.: 63407 Cov.: 32

Gnomad AFR AF: 0.875

Gnomad AMI AF: 0.950

Gnomad AMR AF: 0.909

Gnomad ASJ AF: 0.937

Gnomad EAS AF: 0.979

Gnomad SAS AF: 0.914

Gnomad FIN AF: 0.943

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.925

Gnomad OTH AF: 0.917

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

GnomAD4 genome AF: 0.913 AC: 138878 AN: 152162 Hom.: 63444 Cov.: 32 AF XY: 0.915 AC XY: 68039 AN XY: 74394

African (AFR) AF: 0.875 AC: 36310 AN: 41482

American (AMR) AF: 0.909 AC: 13882 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.937 AC: 3252 AN: 3472

East Asian (EAS) AF: 0.979 AC: 5064 AN: 5174

South Asian (SAS) AF: 0.914 AC: 4402 AN: 4818

European-Finnish (FIN) AF: 0.943 AC: 10006 AN: 10610

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.925 AC: 62882 AN: 68012

Other (OTH) AF: 0.915 AC: 1935 AN: 2114

Alfa AF: 0.922 Hom.: 89184

Bravo AF: 0.911

Asia WGS AF: 0.915 AC: 3183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.0
DANN	Benign	0.37
PhyloP100		0.93

Splicing

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

Other links and lift over

dbSNP: rs4642724; hg19: chr9-122481907;