chr8-92570115-A-G

Variant names:

• chr8-92570115-A-G
• rs1839263
• ENST00000523284.3:n.480-1049T>C

Variant summary

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

The ENST00000523284.3(ENSG00000253634):​n.480-1049T>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: ENSG00000253634 ENST00000523284.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.241
• Publications: 0 publications found

Genes affected

ENSG00000253634 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000523284.3. 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
	LOC102724710	NR_125827.1		n.396-1049T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253634	ENST00000523284.3	TSL:3	n.480-1049T>C		intron	N/A
	ENSG00000253634	ENST00000648652.1		n.471-1049T>C		intron	N/A
	ENSG00000253634	ENST00000653143.2		n.484-1049T>C		intron	N/A

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

African (AFR) AF: 0.00342 AC: 142 AN: 41572

American (AMR) AF: 0.0879 AC: 1341 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.00894 AC: 31 AN: 3468

East Asian (EAS) AF: 0.374 AC: 1923 AN: 5140

South Asian (SAS) AF: 0.152 AC: 731 AN: 4824

European-Finnish (FIN) AF: 0.0331 AC: 352 AN: 10620

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.00166 AC: 113 AN: 67994

Other (OTH) AF: 0.0384 AC: 81 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.2
DANN	Benign	0.68
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs1839263; hg19: chr8-93582343;