ENST00000532929.1:n.252+8348A>G

Variant names:

• chr11-109504243-T-C
• rs10502118
• ENST00000532929.1:n.252+8348A>G

Variant summary

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

The ENST00000532929.1(ENSG00000255028):​n.252+8348A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0836 in 152,176 control chromosomes in the GnomAD database, including 910 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 0.084 (910 hom., cov: 32)
• Consequence: ENSG00000255028 ENST00000532929.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.72

Genes affected

ENSG00000255028 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.195 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
ENSG00000255028	ENST00000532929.1	n.252+8348A>G		intron_variant	Intron 2 of 3	3
ENSG00000255028	ENST00000532992.5	n.427+8336A>G		intron_variant	Intron 3 of 4	4

Frequencies

GnomAD3 genomes AF: 0.0835 AC: 12694 AN: 152058 Hom.: 904 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0653

Gnomad ASJ AF: 0.0424

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.00952

Gnomad FIN AF: 0.0312

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0405

Gnomad OTH AF: 0.0718

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

GnomAD4 genome AF: 0.0836 AC: 12728 AN: 152176 Hom.: 910 Cov.: 32 AF XY: 0.0816 AC XY: 6072 AN XY: 74416

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.0653

Gnomad4 ASJ AF: 0.0424

Gnomad4 EAS AF: 0.00155

Gnomad4 SAS AF: 0.00953

Gnomad4 FIN AF: 0.0312

Gnomad4 NFE AF: 0.0405

Gnomad4 OTH AF: 0.0706

Alfa AF: 0.0575 Hom.: 156

Bravo AF: 0.0926

Asia WGS AF: 0.0250 AC: 87 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.25
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10502118; hg19: chr11-109374969;