chr9-27586164-A-G

Variant names:

• chr9-27586164-A-G
• rs2453556
• ENST00000827310.1:n.919T>C

Variant summary

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

The ENST00000827310.1(ENSG00000307594):​n.919T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 151,930 control chromosomes in the GnomAD database, including 16,362 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 0.46 (16362 hom., cov: 31)
• Consequence: ENSG00000307594 ENST00000827310.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.816
• Publications: 16 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000827310.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307594	ENST00000827310.1		n.919T>C		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000307594	ENST00000827311.1		n.611T>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000307594	ENST00000827312.1		n.963T>C		non_coding_transcript_exon	Exon 5 of 5

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69286 AN: 151812 Hom.: 16335 Cov.: 31

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.457 AC: 69370 AN: 151930 Hom.: 16362 Cov.: 31 AF XY: 0.456 AC XY: 33872 AN XY: 74302

African (AFR) AF: 0.584 AC: 24155 AN: 41380

American (AMR) AF: 0.435 AC: 6658 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1109 AN: 3472

East Asian (EAS) AF: 0.463 AC: 2385 AN: 5146

South Asian (SAS) AF: 0.407 AC: 1959 AN: 4818

European-Finnish (FIN) AF: 0.403 AC: 4261 AN: 10578

Middle Eastern (MID) AF: 0.363 AC: 106 AN: 292

European-Non Finnish (NFE) AF: 0.403 AC: 27370 AN: 67934

Other (OTH) AF: 0.443 AC: 934 AN: 2108

Alfa AF: 0.422 Hom.: 45726

Bravo AF: 0.467

Asia WGS AF: 0.455 AC: 1585 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	14
DANN	Benign	0.72
PhyloP100		0.82

Splicing

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

Other links and lift over

dbSNP: rs2453556; hg19: chr9-27586162;