8-92541230-T-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000253634 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253634	ENST00000648652.1	n.535-24338A>G		intron_variant	Intron 4 of 13

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

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.456

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.355

Alfa AF: 0.386 Hom.: 2423

Bravo AF: 0.349

Asia WGS AF: 0.399 AC: 1383 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1449233; hg19: chr8-93553458;