chr8-92570115-A-G

Position:

• chr8-92570115-A-G

Variant summary

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

The NR_125827.1(LOC102724710):​n.396-1049T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.031 in 152,196 control chromosomes in the GnomAD database, including 541 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 0.031 (541 hom., cov: 32)
• Consequence: LOC102724710 NR_125827.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.241

Genes affected

ENSG00000253634 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102724710	NR_125827.1	n.396-1049T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000253634	ENST00000523284.2	n.478-1049T>C		intron_variant		3
ENSG00000253634	ENST00000648652.1	n.471-1049T>C		intron_variant
ENSG00000253634	ENST00000653143.1	n.482-1049T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0310 AC: 4708 AN: 152080 Hom.: 539 Cov.: 32

Gnomad AFR AF: 0.00343

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0874

Gnomad ASJ AF: 0.00894

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.0331

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00166

Gnomad OTH AF: 0.0344

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

GnomAD4 genome AF: 0.0310 AC: 4716 AN: 152196 Hom.: 541 Cov.: 32 AF XY: 0.0369 AC XY: 2743 AN XY: 74406

Gnomad4 AFR AF: 0.00342

Gnomad4 AMR AF: 0.0879

Gnomad4 ASJ AF: 0.00894

Gnomad4 EAS AF: 0.374

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.0331

Gnomad4 NFE AF: 0.00166

Gnomad4 OTH AF: 0.0384

Alfa AF: 0.0155 Hom.: 23

Bravo AF: 0.0355

Asia WGS AF: 0.258 AC: 892 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.2
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1839263; hg19: chr8-93582343;