chr8-51304202-T-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000253664 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253664	ENST00000521294.1	n.121-16518T>C		intron_variant	Intron 1 of 1	2

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

Gnomad4 AFR AF: 0.543

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.280

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.222

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.320

Alfa AF: 0.265 Hom.: 6854

Bravo AF: 0.340

Asia WGS AF: 0.238 AC: 829 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7821565; hg19: chr8-52216762;