rs4424056

Variant names:

• chr6-91135689-T-G
• rs4424056
• ENST00000828793.1:n.371-8984T>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000828793.1(ENSG00000307789):​n.371-8984T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.768 in 152,096 control chromosomes in the GnomAD database, including 45,299 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 0.77 (45299 hom., cov: 33)
• Consequence: ENSG00000307789 ENST00000828793.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.08
• Publications: 2 publications found

Genes affected

ENSG00000307789 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 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
ENSG00000307789	ENST00000828793.1	n.371-8984T>G		intron_variant	Intron 3 of 3
ENSG00000307789	ENST00000828794.1	n.606-8984T>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.768 AC: 116781 AN: 151978 Hom.: 45262 Cov.: 33

Gnomad AFR AF: 0.688

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.847

Gnomad FIN AF: 0.788

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.751

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

GnomAD4 genome AF: 0.768 AC: 116866 AN: 152096 Hom.: 45299 Cov.: 33 AF XY: 0.772 AC XY: 57399 AN XY: 74350

African (AFR) AF: 0.688 AC: 28515 AN: 41448

American (AMR) AF: 0.805 AC: 12300 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.798 AC: 2766 AN: 3466

East Asian (EAS) AF: 0.960 AC: 4958 AN: 5164

South Asian (SAS) AF: 0.847 AC: 4088 AN: 4828

European-Finnish (FIN) AF: 0.788 AC: 8351 AN: 10596

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.786 AC: 53467 AN: 67992

Other (OTH) AF: 0.754 AC: 1593 AN: 2114

Alfa AF: 0.785 Hom.: 185803

Bravo AF: 0.764

Asia WGS AF: 0.893 AC: 3101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	23
DANN	Benign	0.80
PhyloP100		3.1

Splicing

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

Other links and lift over

dbSNP: rs4424056; hg19: chr6-91845407;