8-57566364-T-C

Variant names:

• chr8-57566364-T-C
• rs9297980
• ENST00000520881.2:n.485-25116T>C

Variant summary

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

The ENST00000520881.2(ENSG00000253821):​n.485-25116T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 151,518 control chromosomes in the GnomAD database, including 15,341 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 0.44 (15341 hom., cov: 33)
• Consequence: ENSG00000253821 ENST00000520881.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.935
• Publications: 0 publications found

Genes affected

ENSG00000253821 (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 (SAS) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000520881.2. 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
	ENSG00000253821	ENST00000520881.2	TSL:5	n.485-25116T>C		intron	N/A
	ENSG00000253821	ENST00000796108.1		n.322-25116T>C		intron	N/A
	ENSG00000253821	ENST00000796110.1		n.142-25116T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67076 AN: 151404 Hom.: 15332 Cov.: 33

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.443 AC: 67112 AN: 151518 Hom.: 15341 Cov.: 33 AF XY: 0.446 AC XY: 33042 AN XY: 74018

African (AFR) AF: 0.323 AC: 13403 AN: 41434

American (AMR) AF: 0.446 AC: 6788 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1631 AN: 3462

East Asian (EAS) AF: 0.641 AC: 3304 AN: 5154

South Asian (SAS) AF: 0.647 AC: 3111 AN: 4806

European-Finnish (FIN) AF: 0.474 AC: 4955 AN: 10460

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.477 AC: 32290 AN: 67682

Other (OTH) AF: 0.460 AC: 966 AN: 2102

Alfa AF: 0.469 Hom.: 50171

Bravo AF: 0.433

Asia WGS AF: 0.598 AC: 2077 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.58
DANN	Benign	0.46
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs9297980; hg19: chr8-58478923;