9-27589659-A-G

Variant names:

• chr9-27589659-A-G
• rs696826
• ENST00000827310.1:n.697-3273T>C

Variant summary

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

The ENST00000827310.1(ENSG00000307594):​n.697-3273T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.844 in 152,250 control chromosomes in the GnomAD database, including 54,362 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 0.84 (54362 hom., cov: 34)
• Consequence: ENSG00000307594 ENST00000827310.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 7 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.966 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.697-3273T>C		intron_variant	Intron 3 of 3
ENSG00000307594	ENST00000827311.1	n.389-3273T>C		intron_variant	Intron 1 of 1
ENSG00000307594	ENST00000827312.1	n.741-3273T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.845 AC: 128481 AN: 152132 Hom.: 54338 Cov.: 34

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.876

Gnomad ASJ AF: 0.844

Gnomad EAS AF: 0.989

Gnomad SAS AF: 0.933

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.845

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

GnomAD4 genome AF: 0.844 AC: 128555 AN: 152250 Hom.: 54362 Cov.: 34 AF XY: 0.847 AC XY: 63081 AN XY: 74446

African (AFR) AF: 0.816 AC: 33899 AN: 41540

American (AMR) AF: 0.877 AC: 13420 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.844 AC: 2932 AN: 3472

East Asian (EAS) AF: 0.989 AC: 5116 AN: 5174

South Asian (SAS) AF: 0.932 AC: 4498 AN: 4824

European-Finnish (FIN) AF: 0.835 AC: 8848 AN: 10600

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.839 AC: 57038 AN: 68012

Other (OTH) AF: 0.845 AC: 1787 AN: 2114

Alfa AF: 0.838 Hom.: 36167

Bravo AF: 0.845

Asia WGS AF: 0.936 AC: 3257 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	2.8
DANN	Benign	0.50
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs696826; hg19: chr9-27589657; COSMIC: COSV60346998;