rs9824873

Variant names:

• chr3-183583986-T-C
• rs9824873
• ENST00000727232.1:n.149+182A>G

Variant summary

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

The ENST00000727232.1(ENSG00000295000):​n.149+182A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 152,140 control chromosomes in the GnomAD database, including 10,130 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 0.34 (10130 hom., cov: 33)
• Consequence: ENSG00000295000 ENST00000727232.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544
• Publications: 6 publications found

Genes affected

ENSG00000295000 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295000	ENST00000727232.1	n.149+182A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51582 AN: 152022 Hom.: 10103 Cov.: 33

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.340 AC: 51665 AN: 152140 Hom.: 10130 Cov.: 33 AF XY: 0.338 AC XY: 25131 AN XY: 74388

African (AFR) AF: 0.548 AC: 22741 AN: 41494

American (AMR) AF: 0.282 AC: 4308 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 895 AN: 3470

East Asian (EAS) AF: 0.310 AC: 1602 AN: 5174

South Asian (SAS) AF: 0.272 AC: 1315 AN: 4826

European-Finnish (FIN) AF: 0.303 AC: 3206 AN: 10588

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.241 AC: 16359 AN: 67996

Other (OTH) AF: 0.340 AC: 719 AN: 2116

Alfa AF: 0.266 Hom.: 24790

Bravo AF: 0.349

Asia WGS AF: 0.325 AC: 1127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.8
DANN	Benign	0.73
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs9824873; hg19: chr3-183301774;