rs9284423

Variant names:

• chr18-40422513-T-A
• rs9284423
• ENST00000723683.1:n.331+8792A>T

Your query was ambiguous. Multiple possible variants found:

• chr18-40422513-T-A
• chr18-40422513-T-G

Variant summary

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

The ENST00000723683.1(ENSG00000294453):​n.331+8792A>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 151,978 control chromosomes in the GnomAD database, including 34,701 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 (34701 hom., cov: 32)
• Consequence: ENSG00000294453 ENST00000723683.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23
• Publications: 5 publications found

Genes affected

ENSG00000294453 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.76 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
ENSG00000294453	ENST00000723683.1	n.331+8792A>T		intron_variant	Intron 1 of 2
ENSG00000294453	ENST00000723684.1	n.253+8792A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.674 AC: 102368 AN: 151860 Hom.: 34675 Cov.: 32

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.711

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.677

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

GnomAD4 genome AF: 0.674 AC: 102445 AN: 151978 Hom.: 34701 Cov.: 32 AF XY: 0.677 AC XY: 50255 AN XY: 74262

African (AFR) AF: 0.638 AC: 26453 AN: 41434

American (AMR) AF: 0.740 AC: 11293 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.711 AC: 2465 AN: 3468

East Asian (EAS) AF: 0.633 AC: 3259 AN: 5150

South Asian (SAS) AF: 0.780 AC: 3757 AN: 4814

European-Finnish (FIN) AF: 0.718 AC: 7578 AN: 10548

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

European-Non Finnish (NFE) AF: 0.670 AC: 45537 AN: 67978

Other (OTH) AF: 0.679 AC: 1435 AN: 2114

Alfa AF: 0.682 Hom.: 4435

Bravo AF: 0.672

Asia WGS AF: 0.709 AC: 2466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	9.0
DANN	Benign	0.44
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs9284423; hg19: chr18-38002477;