ENST00000521294.1:n.121-16518T>C

Variant names:

• chr8-51304202-T-C
• rs7821565
• ENST00000521294.1:n.121-16518T>C

Variant summary

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

The ENST00000521294.1(ENSG00000253664):​n.121-16518T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 151,976 control chromosomes in the GnomAD database, including 9,721 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 0.33 (9721 hom., cov: 31)
• Consequence: ENSG00000253664 ENST00000521294.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 8 publications found

Genes affected

ENSG00000253664 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000521294.1. 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
	ENSG00000253664	ENST00000521294.1	TSL:2	n.121-16518T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.329 AC: 50035 AN: 151858 Hom.: 9685 Cov.: 31

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.330 AC: 50124 AN: 151976 Hom.: 9721 Cov.: 31 AF XY: 0.322 AC XY: 23947 AN XY: 74270

African (AFR) AF: 0.543 AC: 22492 AN: 41416

American (AMR) AF: 0.250 AC: 3810 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 969 AN: 3466

East Asian (EAS) AF: 0.141 AC: 731 AN: 5168

South Asian (SAS) AF: 0.218 AC: 1049 AN: 4820

European-Finnish (FIN) AF: 0.222 AC: 2338 AN: 10544

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17799 AN: 67974

Other (OTH) AF: 0.320 AC: 676 AN: 2114

Alfa AF: 0.288 Hom.: 12850

Bravo AF: 0.340

Asia WGS AF: 0.238 AC: 829 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.26
DANN	Benign	0.69
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7821565; hg19: chr8-52216762;