rs842304

Variant names:

• chr9-7682601-C-A
• rs842304
• ENST00000791473.1:n.247+24841C>A

Your query was ambiguous. Multiple possible variants found:

• chr9-7682601-C-A
• chr9-7682601-C-G
• chr9-7682601-C-T

Variant summary

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

The ENST00000791473.1(ENSG00000303045):​n.247+24841C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 152,078 control chromosomes in the GnomAD database, including 12,455 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 0.40 (12455 hom., cov: 33)
• Consequence: ENSG00000303045 ENST00000791473.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.631
• Publications: 11 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.609 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902118	XR_007061415.1	n.598+24841C>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+24841C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60621 AN: 151960 Hom.: 12433 Cov.: 33

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.399 AC: 60686 AN: 152078 Hom.: 12455 Cov.: 33 AF XY: 0.400 AC XY: 29697 AN XY: 74300

African (AFR) AF: 0.473 AC: 19627 AN: 41488

American (AMR) AF: 0.358 AC: 5470 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1477 AN: 3468

East Asian (EAS) AF: 0.627 AC: 3244 AN: 5170

South Asian (SAS) AF: 0.477 AC: 2295 AN: 4810

European-Finnish (FIN) AF: 0.363 AC: 3836 AN: 10562

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.345 AC: 23455 AN: 67980

Other (OTH) AF: 0.379 AC: 801 AN: 2116

Alfa AF: 0.364 Hom.: 47922

Bravo AF: 0.403

Asia WGS AF: 0.498 AC: 1731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.0
DANN	Benign	0.51
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs842304; hg19: chr9-7682601;