rs9662589

Variant names:

• chr1-232141865-A-C
• rs9662589
• ENST00000733245.1:n.202-10211A>C

Variant summary

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

The ENST00000733245.1(ENSG00000235152):​n.202-10211A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 152,088 control chromosomes in the GnomAD database, including 9,752 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 0.32 (9752 hom., cov: 33)
• Consequence: ENSG00000235152 ENST00000733245.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 8 publications found

Genes affected

ENSG00000235152 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.554 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
ENSG00000235152	ENST00000733245.1	n.202-10211A>C		intron_variant	Intron 2 of 7
ENSG00000235152	ENST00000733246.1	n.259-10211A>C		intron_variant	Intron 1 of 2
ENSG00000235152	ENST00000733247.1	n.254-10211A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49225 AN: 151970 Hom.: 9726 Cov.: 33

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.324 AC: 49311 AN: 152088 Hom.: 9752 Cov.: 33 AF XY: 0.320 AC XY: 23780 AN XY: 74354

African (AFR) AF: 0.560 AC: 23224 AN: 41470

American (AMR) AF: 0.249 AC: 3811 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 598 AN: 3462

East Asian (EAS) AF: 0.375 AC: 1937 AN: 5162

South Asian (SAS) AF: 0.234 AC: 1127 AN: 4820

European-Finnish (FIN) AF: 0.212 AC: 2240 AN: 10580

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.227 AC: 15427 AN: 67994

Other (OTH) AF: 0.283 AC: 597 AN: 2108

Alfa AF: 0.245 Hom.: 3452

Bravo AF: 0.338

Asia WGS AF: 0.306 AC: 1065 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.49
DANN	Benign	0.53
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs9662589; hg19: chr1-232277611;