rs62526245

Positions:

• chr8-84016901-C-A

Variant summary

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

The ENST00000523678.1(ENSG00000254202):​n.124-27643C>A 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 0.378 in 151,842 control chromosomes in the GnomAD database, including 11,775 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 0.38 (11775 hom., cov: 31)
• Consequence: ENST00000523678.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.573 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
	ENST00000523678.1	n.124-27643C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57243 AN: 151724 Hom.: 11743 Cov.: 31

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.378 AC: 57338 AN: 151842 Hom.: 11775 Cov.: 31 AF XY: 0.380 AC XY: 28184 AN XY: 74222

Gnomad4 AFR AF: 0.536

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.591

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.355

Alfa AF: 0.332 Hom.: 1122

Bravo AF: 0.388

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.33
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs62526245; hg19: chr8-84929136;