8-82521385-G-C

Variant names:

• chr8-82521385-G-C
• rs6986026
• ENST00000522776.5:n.450+1848C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000522776.5(ENSG00000253503):​n.450+1848C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 151,960 control chromosomes in the GnomAD database, including 10,259 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 0.32 (10259 hom., cov: 33)
• Consequence: ENSG00000253503 ENST00000522776.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200
• Publications: 1 publications found

Genes affected

ENSG00000253503 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000522776.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253503	ENST00000522776.5	TSL:4	n.450+1848C>G		intron	N/A
	ENSG00000254394	ENST00000658531.1		n.149+33112G>C		intron	N/A
	ENSG00000254394	ENST00000659043.1		n.387-18531G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48963 AN: 151840 Hom.: 10229 Cov.: 33

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.323 AC: 49040 AN: 151960 Hom.: 10259 Cov.: 33 AF XY: 0.325 AC XY: 24117 AN XY: 74272

African (AFR) AF: 0.573 AC: 23738 AN: 41410

American (AMR) AF: 0.384 AC: 5869 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 716 AN: 3470

East Asian (EAS) AF: 0.474 AC: 2445 AN: 5156

South Asian (SAS) AF: 0.203 AC: 978 AN: 4818

European-Finnish (FIN) AF: 0.223 AC: 2349 AN: 10550

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.179 AC: 12140 AN: 67970

Other (OTH) AF: 0.299 AC: 631 AN: 2112

Alfa AF: 0.252 Hom.: 808

Bravo AF: 0.348

Asia WGS AF: 0.362 AC: 1258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.68
DANN	Benign	0.31
PhyloP100		-0.0020

Splicing

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

Other links and lift over

dbSNP: rs6986026; hg19: chr8-83433620;