rs6982367

Positions:

• chr8-57608778-T-C

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, non coding transcript 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: ENST00000520426.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000520426.1	n.274-14316A>G		intron_variant, non_coding_transcript_variant		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;