ENST00000522776.5:n.451-1018T>C

Variant names:

• chr8-82515679-A-G
• rs2137962
• ENST00000522776.5:n.451-1018T>C

Variant summary

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

The ENST00000522776.5(ENSG00000253503):​n.451-1018T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.636 in 151,998 control chromosomes in the GnomAD database, including 32,662 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 0.64 (32662 hom., cov: 32)
• Consequence: ENSG00000253503 ENST00000522776.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.844
• Publications: 7 publications found

Genes affected

ENSG00000253503 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.911 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000522776.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253503	ENST00000522776.5	TSL:4	n.451-1018T>C		intron	N/A
	ENSG00000254394	ENST00000658531.1		n.149+27406A>G		intron	N/A
	ENSG00000254394	ENST00000659043.1		n.387-24237A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.635 AC: 96476 AN: 151880 Hom.: 32599 Cov.: 32

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.933

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.636 AC: 96603 AN: 151998 Hom.: 32662 Cov.: 32 AF XY: 0.639 AC XY: 47492 AN XY: 74296

African (AFR) AF: 0.854 AC: 35451 AN: 41498

American (AMR) AF: 0.633 AC: 9644 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1617 AN: 3466

East Asian (EAS) AF: 0.933 AC: 4811 AN: 5156

South Asian (SAS) AF: 0.630 AC: 3046 AN: 4832

European-Finnish (FIN) AF: 0.565 AC: 5972 AN: 10572

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.503 AC: 34142 AN: 67914

Other (OTH) AF: 0.614 AC: 1297 AN: 2112

Alfa AF: 0.545 Hom.: 99793

Bravo AF: 0.652

Asia WGS AF: 0.781 AC: 2713 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.71
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs2137962; hg19: chr8-83427914;