ENST00000840715.1:n.334+2850A>G

Variant names:

• chr9-120111878-T-C
• rs945246
• ENST00000840715.1:n.334+2850A>G

Variant summary

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

The ENST00000840715.1(ENSG00000309396):​n.334+2850A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.553 in 152,118 control chromosomes in the GnomAD database, including 23,335 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 0.55 (23335 hom., cov: 33)
• Consequence: ENSG00000309396 ENST00000840715.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12
• Publications: 5 publications found

Genes affected

ENSG00000309396 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.589 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
ENSG00000309396	ENST00000840715.1	n.334+2850A>G		intron_variant	Intron 2 of 4
ENSG00000309396	ENST00000840716.1	n.244+8784A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.553 AC: 84000 AN: 152000 Hom.: 23311 Cov.: 33

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.553 AC: 84079 AN: 152118 Hom.: 23335 Cov.: 33 AF XY: 0.552 AC XY: 41038 AN XY: 74366

African (AFR) AF: 0.595 AC: 24677 AN: 41478

American (AMR) AF: 0.566 AC: 8652 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2176 AN: 3470

East Asian (EAS) AF: 0.604 AC: 3129 AN: 5182

South Asian (SAS) AF: 0.515 AC: 2481 AN: 4818

European-Finnish (FIN) AF: 0.507 AC: 5355 AN: 10566

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.525 AC: 35698 AN: 68004

Other (OTH) AF: 0.571 AC: 1207 AN: 2112

Alfa AF: 0.532 Hom.: 90146

Bravo AF: 0.562

Asia WGS AF: 0.547 AC: 1903 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.40
DANN	Benign	0.75
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs945246; hg19: chr9-122874156; COSMIC: COSV60400430;