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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000791473.1. 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
	ENSG00000303045	ENST00000791473.1		n.247+24841C>A		intron	N/A

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 v4.9

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

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

Other links and lift over

dbSNP: rs842304;

hg19: chr9-7682601;