rs619589

Variant names:

• chr9-29543981-C-T
• rs619589
• ENST00000850880.1:n.99-8786C>T

Variant summary

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

The ENST00000850880.1(ENSG00000300941):​n.99-8786C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.604 in 151,582 control chromosomes in the GnomAD database, including 28,325 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 0.60 (28325 hom., cov: 32)
• Consequence: ENSG00000300941 ENST00000850880.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.771
• Publications: 2 publications found

Genes affected

ENSG00000300941 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.793 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
ENSG00000300941	ENST00000850880.1	n.99-8786C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91397 AN: 151464 Hom.: 28281 Cov.: 32

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.814

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.604 AC: 91506 AN: 151582 Hom.: 28325 Cov.: 32 AF XY: 0.605 AC XY: 44791 AN XY: 74054

African (AFR) AF: 0.725 AC: 30008 AN: 41414

American (AMR) AF: 0.598 AC: 9072 AN: 15164

Ashkenazi Jewish (ASJ) AF: 0.481 AC: 1666 AN: 3462

East Asian (EAS) AF: 0.814 AC: 4197 AN: 5158

South Asian (SAS) AF: 0.566 AC: 2729 AN: 4820

European-Finnish (FIN) AF: 0.595 AC: 6261 AN: 10526

Middle Eastern (MID) AF: 0.507 AC: 147 AN: 290

European-Non Finnish (NFE) AF: 0.526 AC: 35612 AN: 67736

Other (OTH) AF: 0.597 AC: 1255 AN: 2102

Alfa AF: 0.543 Hom.: 11561

Bravo AF: 0.611

Asia WGS AF: 0.693 AC: 2397 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.2
DANN	Benign	0.64
PhyloP100		0.77

Splicing

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

Other links and lift over

dbSNP: rs619589; hg19: chr9-29543979;