rs2289599

Variant names:

• chr5-77912325-A-G
• rs2289599
• ENST00000719931.1:n.340+8485T>C

Your query was ambiguous. Multiple possible variants found:

• chr5-77912325-A-G
• chr5-77912325-A-T

Variant summary

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

The ENST00000719931.1(ENSG00000293921):​n.340+8485T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.794 in 152,116 control chromosomes in the GnomAD database, including 48,714 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 0.79 (48714 hom., cov: 31)
• Consequence: ENSG00000293921 ENST00000719931.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.963
• Publications: 4 publications found

Genes affected

ENSG00000293921 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929154	NR_105012.1	n.170+27500A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293921	ENST00000719931.1	n.340+8485T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.794 AC: 120633 AN: 151998 Hom.: 48667 Cov.: 31

Gnomad AFR AF: 0.945

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.894

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.792

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

GnomAD4 genome AF: 0.794 AC: 120740 AN: 152116 Hom.: 48714 Cov.: 31 AF XY: 0.795 AC XY: 59099 AN XY: 74332

African (AFR) AF: 0.945 AC: 39241 AN: 41524

American (AMR) AF: 0.820 AC: 12524 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.778 AC: 2700 AN: 3470

East Asian (EAS) AF: 0.894 AC: 4620 AN: 5166

South Asian (SAS) AF: 0.734 AC: 3539 AN: 4822

European-Finnish (FIN) AF: 0.734 AC: 7762 AN: 10570

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.704 AC: 47870 AN: 67972

Other (OTH) AF: 0.789 AC: 1664 AN: 2110

Alfa AF: 0.728 Hom.: 67536

Bravo AF: 0.811

Asia WGS AF: 0.801 AC: 2787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0060
DANN	Benign	0.43
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs2289599; hg19: chr5-77208149;