rs1889055

Variant names:

• chr9-29539921-A-G
• rs1889055
• ENST00000850880.1:n.99-12846A>G

Your query was ambiguous. Multiple possible variants found:

• chr9-29539921-A-G
• chr9-29539921-A-T

Variant summary

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

The ENST00000850880.1(ENSG00000300941):​n.99-12846A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 151,494 control chromosomes in the GnomAD database, including 12,255 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 0.39 (12255 hom., cov: 32)
• Consequence: ENSG00000300941 ENST00000850880.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.453
• Publications: 4 publications found

Genes affected

ENSG00000300941 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.449 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
ENSG00000300941	ENST00000850880.1	n.99-12846A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59446 AN: 151376 Hom.: 12258 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.393 AC: 59468 AN: 151494 Hom.: 12255 Cov.: 32 AF XY: 0.394 AC XY: 29174 AN XY: 74016

African (AFR) AF: 0.277 AC: 11498 AN: 41438

American (AMR) AF: 0.431 AC: 6533 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1567 AN: 3456

East Asian (EAS) AF: 0.192 AC: 989 AN: 5152

South Asian (SAS) AF: 0.349 AC: 1681 AN: 4820

European-Finnish (FIN) AF: 0.506 AC: 5341 AN: 10558

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.454 AC: 30666 AN: 67592

Other (OTH) AF: 0.408 AC: 858 AN: 2102

Alfa AF: 0.430 Hom.: 46583

Bravo AF: 0.384

Asia WGS AF: 0.318 AC: 1105 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	7.4
DANN	Benign	0.47
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs1889055; hg19: chr9-29539919; COSMIC: COSV60348467;