chr8-27596246-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901919	XR_007060868.1	n.1398-821C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300853	ENST00000774578.1	n.170-821C>T		intron_variant	Intron 1 of 1
ENSG00000300853	ENST00000774579.1	n.285-821C>T		intron_variant	Intron 1 of 1
ENSG00000300853	ENST00000774580.1	n.129-821C>T		intron_variant	Intron 1 of 1
ENSG00000300853	ENST00000774581.1	n.403-821C>T		intron_variant	Intron 1 of 1

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 v4.3

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;