ENST00000842803.1:n.412+789A>G

Variant names:

• chr7-44994240-T-C
• rs4724339
• ENST00000842803.1:n.412+789A>G

Variant summary

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

The ENST00000842803.1(ENSG00000309655):​n.412+789A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 150,378 control chromosomes in the GnomAD database, including 19,383 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 0.49 (19383 hom., cov: 29)
• Consequence: ENSG00000309655 ENST00000842803.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14
• Publications: 1 publications found

Genes affected

ENSG00000309655 (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 (EAS) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000842803.1. 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
	ENSG00000309655	ENST00000842803.1		n.412+789A>G		intron	N/A
	ENSG00000309655	ENST00000842804.1		n.505+789A>G		intron	N/A
	ENSG00000309655	ENST00000842805.1		n.392+789A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.489 AC: 73450 AN: 150266 Hom.: 19381 Cov.: 29

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.542

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.489 AC: 73464 AN: 150378 Hom.: 19383 Cov.: 29 AF XY: 0.493 AC XY: 36051 AN XY: 73138

African (AFR) AF: 0.280 AC: 11460 AN: 40932

American (AMR) AF: 0.500 AC: 7536 AN: 15084

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1845 AN: 3470

East Asian (EAS) AF: 0.737 AC: 3760 AN: 5102

South Asian (SAS) AF: 0.436 AC: 2086 AN: 4782

European-Finnish (FIN) AF: 0.652 AC: 6431 AN: 9864

Middle Eastern (MID) AF: 0.541 AC: 157 AN: 290

European-Non Finnish (NFE) AF: 0.567 AC: 38494 AN: 67858

Other (OTH) AF: 0.528 AC: 1102 AN: 2086

Alfa AF: 0.498 Hom.: 2498

Bravo AF: 0.476

Asia WGS AF: 0.539 AC: 1874 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.8
DANN	Benign	0.78
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs4724339; hg19: chr7-45033839;