rs12000445

Variant names:

• chr9-23426273-A-G
• rs12000445
• ENST00000640003.1:n.139+12289T>C

Variant summary

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

The ENST00000640003.1(ENSG00000284418):​n.139+12289T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,120 control chromosomes in the GnomAD database, including 3,890 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 0.18 (3890 hom., cov: 32)
• Consequence: ENSG00000284418 ENST00000640003.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.337
• Publications: 8 publications found

Genes affected

ENSG00000284418 (HGNC:58153):

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 = 0.389 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
ENSG00000284418	ENST00000640003.1	n.139+12289T>C		intron_variant	Intron 1 of 9	5
ENSG00000284418	ENST00000664493.1	n.110+12289T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26879 AN: 152002 Hom.: 3890 Cov.: 32

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.0426

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.0687

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.177 AC: 26904 AN: 152120 Hom.: 3890 Cov.: 32 AF XY: 0.175 AC XY: 13013 AN XY: 74390

African (AFR) AF: 0.394 AC: 16341 AN: 41472

American (AMR) AF: 0.160 AC: 2449 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 403 AN: 3468

East Asian (EAS) AF: 0.256 AC: 1320 AN: 5164

South Asian (SAS) AF: 0.155 AC: 749 AN: 4826

European-Finnish (FIN) AF: 0.0426 AC: 452 AN: 10622

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.0687 AC: 4673 AN: 67974

Other (OTH) AF: 0.173 AC: 365 AN: 2110

Alfa AF: 0.114 Hom.: 3743

Bravo AF: 0.197

Asia WGS AF: 0.212 AC: 740 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	0.62
DANN	Benign	0.65
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs12000445; hg19: chr9-23426271;