ENST00000520582.2:n.653+354A>G

Variant names:

• chr8-8936144-A-G
• rs17700611
• ENST00000520582.2:n.653+354A>G

Variant summary

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

The ENST00000520582.2(ENSG00000293372):​n.653+354A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 151,936 control chromosomes in the GnomAD database, including 9,948 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 0.34 (9948 hom., cov: 31)
• Consequence: ENSG00000293372 ENST00000520582.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.700
• Publications: 12 publications found

Genes affected

ENSG00000293372 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000520582.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293372	ENST00000520582.2	TSL:3	n.653+354A>G		intron	N/A
	ENSG00000293372	ENST00000753008.1		n.614+354A>G		intron	N/A
	ENSG00000293372	ENST00000753009.1		n.427+32588A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51041 AN: 151818 Hom.: 9950 Cov.: 31

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.406

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.336 AC: 51043 AN: 151936 Hom.: 9948 Cov.: 31 AF XY: 0.322 AC XY: 23873 AN XY: 74252

African (AFR) AF: 0.207 AC: 8593 AN: 41440

American (AMR) AF: 0.264 AC: 4024 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1876 AN: 3470

East Asian (EAS) AF: 0.00309 AC: 16 AN: 5184

South Asian (SAS) AF: 0.191 AC: 920 AN: 4814

European-Finnish (FIN) AF: 0.341 AC: 3601 AN: 10550

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.453 AC: 30761 AN: 67924

Other (OTH) AF: 0.364 AC: 765 AN: 2104

Alfa AF: 0.409 Hom.: 41960

Bravo AF: 0.323

Asia WGS AF: 0.109 AC: 384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.33
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs17700611; hg19: chr8-8793654;