rs9899891

Variant names:

• chr17-14726429-G-A
• rs9899891
• ENST00000455092.1:n.130+571G>A

Your query was ambiguous. Multiple possible variants found:

• chr17-14726429-G-A
• chr17-14726429-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000455092.1(ENSG00000226130):​n.130+571G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.687 in 152,018 control chromosomes in the GnomAD database, including 36,070 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 0.69 (36070 hom., cov: 32)
• Consequence: ENSG00000226130 ENST00000455092.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0600

Genes affected

ENSG00000226130 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.702 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
ENSG00000226130	ENST00000455092.1	n.130+571G>A		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.687 AC: 104327 AN: 151900 Hom.: 36077 Cov.: 32

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.688

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.687 AC: 104361 AN: 152018 Hom.: 36070 Cov.: 32 AF XY: 0.689 AC XY: 51163 AN XY: 74306

Gnomad4 AFR AF: 0.625

Gnomad4 AMR AF: 0.687

Gnomad4 ASJ AF: 0.719

Gnomad4 EAS AF: 0.720

Gnomad4 SAS AF: 0.683

Gnomad4 FIN AF: 0.780

Gnomad4 NFE AF: 0.707

Gnomad4 OTH AF: 0.688

Alfa AF: 0.696 Hom.: 62948

Bravo AF: 0.678

Asia WGS AF: 0.722 AC: 2511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9899891; hg19: chr17-14629746;