chr8-2797033-C-T

Variant names:

• chr8-2797033-C-T
• rs1026374
• ENST00000520024.1:n.177-7553C>T

Variant summary

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

The ENST00000520024.1(ENSG00000253853):​n.177-7553C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 151,970 control chromosomes in the GnomAD database, including 13,467 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 0.36 (13467 hom., cov: 31)
• Consequence: ENSG00000253853 ENST00000520024.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 2 publications found

Genes affected

ENSG00000253853 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000520024.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105377785	NR_168441.1		n.539-7553C>T		intron	N/A
	LOC105377785	NR_168442.1		n.539-7553C>T		intron	N/A
	LOC105377785	NR_168443.1		n.539-7553C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253853	ENST00000520024.1	TSL:3	n.177-7553C>T		intron	N/A
	ENSG00000253853	ENST00000654515.1		n.532-7553C>T		intron	N/A
	ENSG00000253853	ENST00000662575.1		n.81+1658C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.362 AC: 55019 AN: 151856 Hom.: 13427 Cov.: 31

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.363 AC: 55120 AN: 151970 Hom.: 13467 Cov.: 31 AF XY: 0.365 AC XY: 27104 AN XY: 74290

African (AFR) AF: 0.674 AC: 27919 AN: 41432

American (AMR) AF: 0.458 AC: 6996 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 911 AN: 3462

East Asian (EAS) AF: 0.391 AC: 2010 AN: 5146

South Asian (SAS) AF: 0.284 AC: 1364 AN: 4804

European-Finnish (FIN) AF: 0.186 AC: 1963 AN: 10560

Middle Eastern (MID) AF: 0.366 AC: 107 AN: 292

European-Non Finnish (NFE) AF: 0.190 AC: 12910 AN: 67980

Other (OTH) AF: 0.332 AC: 701 AN: 2110

Alfa AF: 0.261 Hom.: 4326

Bravo AF: 0.405

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.45
DANN	Benign	0.63
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1026374; hg19: chr8-2654569;