rs7821565

Positions:

• chr8-51304202-T-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, non coding transcript 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: ENST00000521294.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000521294.1	n.121-16518T>C		intron_variant, non_coding_transcript_variant		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;