rs888229

Variant names:

• chr9-126156171-G-A
• rs888229
• ENST00000441473.1:n.236-3362G>A

Your query was ambiguous. Multiple possible variants found:

• chr9-126156171-G-A
• chr9-126156171-G-T

Variant summary

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

The ENST00000441473.1(ENSG00000232413):​n.236-3362G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 152,062 control chromosomes in the GnomAD database, including 4,767 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 0.24 (4767 hom., cov: 32)
• Consequence: ENSG00000232413 ENST00000441473.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.50
• Publications: 5 publications found

Genes affected

ENSG00000232413 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.302 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
ENSG00000232413	ENST00000441473.1	n.236-3362G>A		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36989 AN: 151944 Hom.: 4756 Cov.: 32

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.244 AC: 37032 AN: 152062 Hom.: 4767 Cov.: 32 AF XY: 0.242 AC XY: 17998 AN XY: 74330

African (AFR) AF: 0.306 AC: 12697 AN: 41448

American (AMR) AF: 0.253 AC: 3875 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.292 AC: 1012 AN: 3470

East Asian (EAS) AF: 0.273 AC: 1409 AN: 5164

South Asian (SAS) AF: 0.274 AC: 1318 AN: 4812

European-Finnish (FIN) AF: 0.147 AC: 1558 AN: 10578

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14186 AN: 67984

Other (OTH) AF: 0.249 AC: 525 AN: 2112

Alfa AF: 0.201 Hom.: 1703

Bravo AF: 0.255

Asia WGS AF: 0.265 AC: 925 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.091
DANN	Benign	0.54
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs888229; hg19: chr9-128918450;