rs4744369

Variant names:

• chr9-94713114-T-A
• rs4744369
• ENST00000724122.1:n.232+4603A>T

Your query was ambiguous. Multiple possible variants found:

• chr9-94713114-T-A
• chr9-94713114-T-G

Variant summary

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

The ENST00000724122.1(ENSG00000294530):​n.232+4603A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.674 in 152,096 control chromosomes in the GnomAD database, including 35,515 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 0.67 (35515 hom., cov: 32)
• Consequence: ENSG00000294530 ENST00000724122.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.626
• Publications: 6 publications found

Genes affected

ENSG00000294530 (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 (AFR) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000724122.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294530	ENST00000724122.1		n.232+4603A>T		intron	N/A
	ENSG00000294530	ENST00000724123.1		n.226+4603A>T		intron	N/A
	ENSG00000294530	ENST00000724124.1		n.210+4603A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.673 AC: 102338 AN: 151978 Hom.: 35464 Cov.: 32

Gnomad AFR AF: 0.839

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.694

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.674 AC: 102445 AN: 152096 Hom.: 35515 Cov.: 32 AF XY: 0.677 AC XY: 50336 AN XY: 74320

African (AFR) AF: 0.839 AC: 34810 AN: 41478

American (AMR) AF: 0.692 AC: 10581 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1778 AN: 3470

East Asian (EAS) AF: 0.734 AC: 3797 AN: 5172

South Asian (SAS) AF: 0.694 AC: 3345 AN: 4822

European-Finnish (FIN) AF: 0.644 AC: 6784 AN: 10542

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.576 AC: 39170 AN: 68000

Other (OTH) AF: 0.654 AC: 1383 AN: 2114

Alfa AF: 0.453 Hom.: 1081

Bravo AF: 0.685

Asia WGS AF: 0.726 AC: 2525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.8
DANN	Benign	0.62
PhyloP100		0.63

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4744369;

hg19: chr9-97475396;

COSMIC: COSV60380419;