8-27596246-C-T

Variant names:

• chr8-27596246-C-T
• rs2279591
• ENST00000774578.1:n.170-821C>T

Variant summary

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

The ENST00000774578.1(ENSG00000300853):​n.170-821C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,082 control chromosomes in the GnomAD database, including 7,357 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 0.29 (7357 hom., cov: 32)
• Consequence: ENSG00000300853 ENST00000774578.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504
• Publications: 4 publications found

Genes affected

ENSG00000300853 (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 (EAS) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000774578.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300853	ENST00000774578.1		n.170-821C>T		intron	N/A
	ENSG00000300853	ENST00000774579.1		n.285-821C>T		intron	N/A
	ENSG00000300853	ENST00000774580.1		n.129-821C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44245 AN: 151964 Hom.: 7351 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.705

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.291 AC: 44271 AN: 152082 Hom.: 7357 Cov.: 32 AF XY: 0.304 AC XY: 22592 AN XY: 74322

African (AFR) AF: 0.199 AC: 8239 AN: 41486

American (AMR) AF: 0.352 AC: 5373 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 825 AN: 3468

East Asian (EAS) AF: 0.705 AC: 3633 AN: 5154

South Asian (SAS) AF: 0.512 AC: 2464 AN: 4816

European-Finnish (FIN) AF: 0.387 AC: 4087 AN: 10574

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.274 AC: 18648 AN: 67982

Other (OTH) AF: 0.259 AC: 547 AN: 2114

Alfa AF: 0.316 Hom.: 3084

Bravo AF: 0.280

Asia WGS AF: 0.577 AC: 2005 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.9
DANN	Benign	0.65
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs2279591; hg19: chr8-27453763;