8-86206843-A-G

Position:

• chr8-86206843-A-G

Variant summary

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

The ENST00000523112.1(ENSG00000253699):​n.460-5352A>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 0.391 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: ENST00000523112.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.139

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC105375623	XR_928373.4	n.458-5352A>G		intron_variant, non_coding_transcript_variant
LOC105375623	XR_928374.3	n.378-5352A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000523112.1	n.460-5352A>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.521

Gnomad4 AMR AF: 0.446

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.485

Gnomad4 SAS AF: 0.504

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.380

Alfa AF: 0.382 Hom.: 2192

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6470733; hg19: chr8-87219072;