rs2583989

Variant names:

• chr4-89848271-A-G
• rs2583989
• ENST00000776860.1:n.209-7309T>C

Variant summary

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

The ENST00000776860.1(ENSG00000301182):​n.209-7309T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 151,978 control chromosomes in the GnomAD database, including 3,445 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 0.19 (3445 hom., cov: 31)
• Consequence: ENSG00000301182 ENST00000776860.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.703
• Publications: 3 publications found

Genes affected

ENSG00000301182 (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 = 0.265 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
ENSG00000301182	ENST00000776860.1	n.209-7309T>C		intron_variant	Intron 1 of 1
ENSG00000301182	ENST00000776861.1	n.183-7309T>C		intron_variant	Intron 1 of 1
ENSG00000301182	ENST00000776862.1	n.203+6653T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29494 AN: 151860 Hom.: 3442 Cov.: 31

Gnomad AFR AF: 0.0930

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.000966

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.194 AC: 29515 AN: 151978 Hom.: 3445 Cov.: 31 AF XY: 0.192 AC XY: 14250 AN XY: 74280

African (AFR) AF: 0.0930 AC: 3855 AN: 41470

American (AMR) AF: 0.179 AC: 2727 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 714 AN: 3466

East Asian (EAS) AF: 0.000968 AC: 5 AN: 5166

South Asian (SAS) AF: 0.123 AC: 593 AN: 4804

European-Finnish (FIN) AF: 0.243 AC: 2564 AN: 10548

Middle Eastern (MID) AF: 0.158 AC: 46 AN: 292

European-Non Finnish (NFE) AF: 0.268 AC: 18244 AN: 67954

Other (OTH) AF: 0.209 AC: 440 AN: 2108

Alfa AF: 0.224 Hom.: 533

Bravo AF: 0.188

Asia WGS AF: 0.0620 AC: 220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.7
DANN	Benign	0.44
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs2583989; hg19: chr4-90769422;