rs4740904

Variant names:

• chr9-7682860-G-A
• rs4740904
• ENST00000791473.1:n.247+25100G>A

Variant summary

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

The ENST00000791473.1(ENSG00000303045):​n.247+25100G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 152,030 control chromosomes in the GnomAD database, including 16,682 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 0.47 (16682 hom., cov: 33)
• Consequence: ENSG00000303045 ENST00000791473.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.19
• Publications: 1 publications found

Genes affected

ENSG00000303045 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902118	XR_007061415.1	n.598+25100G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303045	ENST00000791473.1	n.247+25100G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.467 AC: 71017 AN: 151912 Hom.: 16668 Cov.: 33

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.468 AC: 71085 AN: 152030 Hom.: 16682 Cov.: 33 AF XY: 0.467 AC XY: 34676 AN XY: 74296

African (AFR) AF: 0.505 AC: 20942 AN: 41440

American (AMR) AF: 0.479 AC: 7325 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1844 AN: 3472

East Asian (EAS) AF: 0.362 AC: 1873 AN: 5170

South Asian (SAS) AF: 0.489 AC: 2358 AN: 4824

European-Finnish (FIN) AF: 0.439 AC: 4631 AN: 10550

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.448 AC: 30459 AN: 67960

Other (OTH) AF: 0.458 AC: 970 AN: 2116

Alfa AF: 0.458 Hom.: 19920

Bravo AF: 0.469

Asia WGS AF: 0.406 AC: 1415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.021
DANN	Benign	0.53
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs4740904; hg19: chr9-7682860; COSMIC: COSV69445396;