rs590299

Variant names:

• chr9-27601572-C-A
• rs590299
• ENST00000827310.1:n.697-15186G>T

Your query was ambiguous. Multiple possible variants found:

• chr9-27601572-C-A
• chr9-27601572-C-T

Variant summary

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

The ENST00000827310.1(ENSG00000307594):​n.697-15186G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 152,074 control chromosomes in the GnomAD database, including 28,830 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 0.61 (28830 hom., cov: 32)
• Consequence: ENSG00000307594 ENST00000827310.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.771
• Publications: 2 publications found

Genes affected

ENSG00000307594 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.74 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
ENSG00000307594	ENST00000827310.1	n.697-15186G>T		intron_variant	Intron 3 of 3
ENSG00000307594	ENST00000827311.1	n.389-15186G>T		intron_variant	Intron 1 of 1
ENSG00000307594	ENST00000827312.1	n.741-15186G>T		intron_variant	Intron 4 of 4
ENSG00000307594	ENST00000827315.1	n.111-15186G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92382 AN: 151956 Hom.: 28797 Cov.: 32

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.773

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.608 AC: 92467 AN: 152074 Hom.: 28830 Cov.: 32 AF XY: 0.606 AC XY: 45020 AN XY: 74340

African (AFR) AF: 0.747 AC: 30984 AN: 41498

American (AMR) AF: 0.494 AC: 7549 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1912 AN: 3468

East Asian (EAS) AF: 0.532 AC: 2753 AN: 5172

South Asian (SAS) AF: 0.469 AC: 2261 AN: 4824

European-Finnish (FIN) AF: 0.619 AC: 6525 AN: 10548

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.565 AC: 38368 AN: 67958

Other (OTH) AF: 0.592 AC: 1251 AN: 2112

Alfa AF: 0.550 Hom.: 2372

Bravo AF: 0.605

Asia WGS AF: 0.496 AC: 1726 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.10
DANN	Benign	0.45
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs590299; hg19: chr9-27601570; COSMIC: COSV60347047;