rs6982367

Variant names:

• chr8-57608778-T-C
• rs6982367
• ENST00000520426.1:n.274-14316A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000520426.1(ENSG00000253322):​n.274-14316A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,130 control chromosomes in the GnomAD database, including 5,657 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 0.18 (5657 hom., cov: 32)
• Consequence: ENSG00000253322 ENST00000520426.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76

Genes affected

ENSG00000253322 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.505 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
ENSG00000253322	ENST00000520426.1	n.274-14316A>G		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26637 AN: 152012 Hom.: 5642 Cov.: 32

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0919

Gnomad ASJ AF: 0.0519

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0118

Gnomad FIN AF: 0.0314

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0473

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.175 AC: 26693 AN: 152130 Hom.: 5657 Cov.: 32 AF XY: 0.170 AC XY: 12680 AN XY: 74410

Gnomad4 AFR AF: 0.511

Gnomad4 AMR AF: 0.0916

Gnomad4 ASJ AF: 0.0519

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0116

Gnomad4 FIN AF: 0.0314

Gnomad4 NFE AF: 0.0472

Gnomad4 OTH AF: 0.142

Alfa AF: 0.0708 Hom.: 1105

Bravo AF: 0.194

Asia WGS AF: 0.0410 AC: 142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.58
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6982367; hg19: chr8-58521337;