rs17219926

Variant names:

• chr9-114817573-T-C
• rs17219926
• ENST00000776746.1:n.453+646A>G

Variant summary

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

The ENST00000776746.1(ENSG00000301160):​n.453+646A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 151,958 control chromosomes in the GnomAD database, including 13,968 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 0.41 (13968 hom., cov: 31)
• Consequence: ENSG00000301160 ENST00000776746.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.201
• Publications: 5 publications found

Genes affected

ENSG00000301160 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.5 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
ENSG00000301160	ENST00000776746.1	n.453+646A>G		intron_variant	Intron 3 of 3
ENSG00000301160	ENST00000776747.1	n.*156A>G		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61805 AN: 151840 Hom.: 13968 Cov.: 31

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.0341

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.407 AC: 61813 AN: 151958 Hom.: 13968 Cov.: 31 AF XY: 0.404 AC XY: 29989 AN XY: 74296

African (AFR) AF: 0.263 AC: 10913 AN: 41440

American (AMR) AF: 0.373 AC: 5698 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 2057 AN: 3464

East Asian (EAS) AF: 0.0336 AC: 174 AN: 5172

South Asian (SAS) AF: 0.432 AC: 2074 AN: 4802

European-Finnish (FIN) AF: 0.500 AC: 5284 AN: 10562

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.504 AC: 34266 AN: 67922

Other (OTH) AF: 0.426 AC: 898 AN: 2110

Alfa AF: 0.453 Hom.: 2097

Bravo AF: 0.388

Asia WGS AF: 0.291 AC: 1011 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.57
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs17219926; hg19: chr9-117579853;