9-27588733-C-A

Variant names:

• chr9-27588733-C-A
• rs702231
• ENST00000827310.1:n.697-2347G>T

Variant summary

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

The ENST00000827310.1(ENSG00000307594):​n.697-2347G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.683 in 151,956 control chromosomes in the GnomAD database, including 35,898 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 0.68 (35898 hom., cov: 31)
• Consequence: ENSG00000307594 ENST00000827310.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.618
• Publications: 8 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.747 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.697-2347G>T		intron_variant	Intron 3 of 3
ENSG00000307594	ENST00000827311.1	n.389-2347G>T		intron_variant	Intron 1 of 1
ENSG00000307594	ENST00000827312.1	n.741-2347G>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.683 AC: 103729 AN: 151838 Hom.: 35900 Cov.: 31

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.803

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.683 AC: 103758 AN: 151956 Hom.: 35898 Cov.: 31 AF XY: 0.681 AC XY: 50603 AN XY: 74274

African (AFR) AF: 0.566 AC: 23428 AN: 41400

American (AMR) AF: 0.640 AC: 9781 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.705 AC: 2446 AN: 3468

East Asian (EAS) AF: 0.635 AC: 3275 AN: 5160

South Asian (SAS) AF: 0.716 AC: 3450 AN: 4820

European-Finnish (FIN) AF: 0.740 AC: 7807 AN: 10550

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.752 AC: 51138 AN: 67962

Other (OTH) AF: 0.687 AC: 1450 AN: 2112

Alfa AF: 0.730 Hom.: 72572

Bravo AF: 0.669

Asia WGS AF: 0.631 AC: 2190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.64
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs702231; hg19: chr9-27588731;