17-14726429-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

Genes affected

ENSG00000226130 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000455092.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000226130	ENST00000455092.1	TSL:3	n.130+571G>A		intron	N/A

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

African (AFR) AF: 0.625 AC: 25910 AN: 41446

American (AMR) AF: 0.687 AC: 10492 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.719 AC: 2494 AN: 3468

East Asian (EAS) AF: 0.720 AC: 3714 AN: 5156

South Asian (SAS) AF: 0.683 AC: 3296 AN: 4828

European-Finnish (FIN) AF: 0.780 AC: 8253 AN: 10578

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.707 AC: 48068 AN: 67968

Other (OTH) AF: 0.688 AC: 1448 AN: 2106

Alfa AF: 0.696 Hom.: 150098

Bravo AF: 0.678

Asia WGS AF: 0.722 AC: 2511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.69
PhyloP100		-0.060

Splicing

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

Other links and lift over

dbSNP: rs9899891; hg19: chr17-14629746;