chr8-86206843-A-G

Variant names:

• chr8-86206843-A-G
• rs6470733
• ENST00000523112.1:n.460-5352A>G

Variant summary

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

The ENST00000523112.1(ENSG00000253699):​n.460-5352A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 151,948 control chromosomes in the GnomAD database, including 12,505 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 0.39 (12505 hom., cov: 32)
• Consequence: ENSG00000253699 ENST00000523112.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.139
• Publications: 3 publications found

Genes affected

ENSG00000253699 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375623	NR_188044.1	n.410-5352A>G		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253699	ENST00000523112.1	n.460-5352A>G		intron_variant	Intron 4 of 4	3
ENSG00000253699	ENST00000809351.1	n.243-5352A>G		intron_variant	Intron 2 of 2
ENSG00000253699	ENST00000809352.1	n.178-5352A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59279 AN: 151830 Hom.: 12457 Cov.: 32

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.391 AC: 59397 AN: 151948 Hom.: 12505 Cov.: 32 AF XY: 0.397 AC XY: 29449 AN XY: 74244

African (AFR) AF: 0.521 AC: 21572 AN: 41414

American (AMR) AF: 0.446 AC: 6800 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 890 AN: 3472

East Asian (EAS) AF: 0.485 AC: 2504 AN: 5162

South Asian (SAS) AF: 0.504 AC: 2426 AN: 4814

European-Finnish (FIN) AF: 0.340 AC: 3592 AN: 10558

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20444 AN: 67972

Other (OTH) AF: 0.380 AC: 802 AN: 2108

Alfa AF: 0.385 Hom.: 2294

Bravo AF: 0.401

Asia WGS AF: 0.500 AC: 1737 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	15
DANN	Benign	0.79
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs6470733; hg19: chr8-87219072;