chr8-92541230-T-C

Variant names:

• chr8-92541230-T-C
• rs1449233
• ENST00000648652.1:n.535-24338A>G

Variant summary

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

The ENST00000648652.1(ENSG00000253634):​n.535-24338A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 152,092 control chromosomes in the GnomAD database, including 11,892 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 0.36 (11892 hom., cov: 32)
• Consequence: ENSG00000253634 ENST00000648652.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.464
• Publications: 1 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648652.1. 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
	ENSG00000253634	ENST00000648652.1		n.535-24338A>G		intron	N/A
	ENSG00000253634	ENST00000744168.1		n.147+27773A>G		intron	N/A
	ENSG00000253634	ENST00000744169.1		n.151-38788A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54684 AN: 151972 Hom.: 11898 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.333

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.359 AC: 54672 AN: 152092 Hom.: 11892 Cov.: 32 AF XY: 0.364 AC XY: 27061 AN XY: 74346

African (AFR) AF: 0.100 AC: 4173 AN: 41534

American (AMR) AF: 0.489 AC: 7460 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1594 AN: 3472

East Asian (EAS) AF: 0.368 AC: 1900 AN: 5164

South Asian (SAS) AF: 0.441 AC: 2124 AN: 4820

European-Finnish (FIN) AF: 0.456 AC: 4816 AN: 10568

Middle Eastern (MID) AF: 0.341 AC: 99 AN: 290

European-Non Finnish (NFE) AF: 0.462 AC: 31399 AN: 67952

Other (OTH) AF: 0.355 AC: 751 AN: 2114

Alfa AF: 0.392 Hom.: 4585

Bravo AF: 0.349

Asia WGS AF: 0.399 AC: 1383 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.7
DANN	Benign	0.34
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs1449233; hg19: chr8-93553458;