ENST00000592809.1:n.176+3319A>G

Variant names:

• chr17-70330197-T-C
• rs312691
• ENST00000592809.1:n.176+3319A>G

Variant summary

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

The ENST00000592809.1(ENSG00000267109):​n.176+3319A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,122 control chromosomes in the GnomAD database, including 4,961 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 0.25 (4961 hom., cov: 32)
• Consequence: ENSG00000267109 ENST00000592809.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.247

Genes affected

ENSG00000267109 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.453 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
ENSG00000267109	ENST00000592809.1	n.176+3319A>G		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37970 AN: 152004 Hom.: 4949 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.250 AC: 37999 AN: 152122 Hom.: 4961 Cov.: 32 AF XY: 0.248 AC XY: 18455 AN XY: 74362

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.469

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.170

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.244

Alfa AF: 0.255 Hom.: 7200

Bravo AF: 0.265

Asia WGS AF: 0.311 AC: 1081 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.6
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs312691; hg19: chr17-68326338;