rs4836817

Variant names:

• chr9-120373094-T-C
• rs4836817
• ENST00000726940.1:n.76+11465A>G

Variant summary

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

The ENST00000726940.1(ENSG00000294948):​n.76+11465A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.757 in 151,952 control chromosomes in the GnomAD database, including 44,387 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 0.76 (44387 hom., cov: 32)
• Consequence: ENSG00000294948 ENST00000726940.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 4 publications found

Genes affected

ENSG00000294948 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.896 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000726940.1. 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
	ENSG00000294948	ENST00000726940.1		n.76+11465A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.757 AC: 114907 AN: 151836 Hom.: 44331 Cov.: 32

Gnomad AFR AF: 0.903

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.851

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.678

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.757 AC: 115021 AN: 151952 Hom.: 44387 Cov.: 32 AF XY: 0.755 AC XY: 56109 AN XY: 74280

African (AFR) AF: 0.903 AC: 37449 AN: 41454

American (AMR) AF: 0.780 AC: 11919 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.695 AC: 2400 AN: 3454

East Asian (EAS) AF: 0.851 AC: 4399 AN: 5172

South Asian (SAS) AF: 0.665 AC: 3197 AN: 4808

European-Finnish (FIN) AF: 0.680 AC: 7198 AN: 10578

Middle Eastern (MID) AF: 0.671 AC: 196 AN: 292

European-Non Finnish (NFE) AF: 0.678 AC: 46046 AN: 67894

Other (OTH) AF: 0.750 AC: 1588 AN: 2116

Alfa AF: 0.717 Hom.: 23478

Bravo AF: 0.775

Asia WGS AF: 0.798 AC: 2704 AN: 3392

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.18
DANN	Benign	0.32
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs4836817; hg19: chr9-123135372;