rs1233579

Variant names:

• chr6-28744886-A-G
• rs1233579
• ENST00000829044.1:n.611+6314A>G

Variant summary

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

The ENST00000829044.1(ENSG00000307816):​n.611+6314A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0701 in 152,240 control chromosomes in the GnomAD database, including 474 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 0.070 (474 hom., cov: 32)
• Consequence: ENSG00000307816 ENST00000829044.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.192
• Publications: 24 publications found

Genes affected

ENSG00000307816 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0873 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
ENSG00000307816	ENST00000829044.1	n.611+6314A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0701 AC: 10662 AN: 152124 Hom.: 473 Cov.: 32

Gnomad AFR AF: 0.0825

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.0287

Gnomad ASJ AF: 0.0259

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00104

Gnomad FIN AF: 0.0394

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0892

Gnomad OTH AF: 0.0488

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

GnomAD4 genome AF: 0.0701 AC: 10666 AN: 152240 Hom.: 474 Cov.: 32 AF XY: 0.0642 AC XY: 4781 AN XY: 74434

African (AFR) AF: 0.0824 AC: 3423 AN: 41534

American (AMR) AF: 0.0286 AC: 438 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0259 AC: 90 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5176

South Asian (SAS) AF: 0.00104 AC: 5 AN: 4824

European-Finnish (FIN) AF: 0.0394 AC: 418 AN: 10608

Middle Eastern (MID) AF: 0.00342 AC: 1 AN: 292

European-Non Finnish (NFE) AF: 0.0891 AC: 6062 AN: 68016

Other (OTH) AF: 0.0482 AC: 102 AN: 2114

Alfa AF: 0.0860 Hom.: 1134

Bravo AF: 0.0709

Asia WGS AF: 0.00491 AC: 18 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.67
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs1233579; hg19: chr6-28712663;