ENST00000527528.1:n.158+9263A>C

Variant names:

• chr11-96599737-A-C
• rs10501861
• ENST00000527528.1:n.158+9263A>C

Variant summary

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

The ENST00000527528.1(ENSG00000254587):​n.158+9263A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.014 in 152,078 control chromosomes in the GnomAD database, including 53 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 0.014 (53 hom., cov: 31)
• Consequence: ENSG00000254587 ENST00000527528.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147

Genes affected

ENSG00000254587 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0521 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
ENSG00000254587	ENST00000527528.1	n.158+9263A>C		intron_variant	Intron 1 of 3	1

Frequencies

GnomAD3 genomes AF: 0.0140 AC: 2128 AN: 151960 Hom.: 51 Cov.: 31

Gnomad AFR AF: 0.00940

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0471

Gnomad ASJ AF: 0.00519

Gnomad EAS AF: 0.0579

Gnomad SAS AF: 0.0263

Gnomad FIN AF: 0.0101

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00632

Gnomad OTH AF: 0.0163

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

GnomAD4 genome AF: 0.0140 AC: 2135 AN: 152078 Hom.: 53 Cov.: 31 AF XY: 0.0149 AC XY: 1109 AN XY: 74332

Gnomad4 AFR AF: 0.00954

Gnomad4 AMR AF: 0.0476

Gnomad4 ASJ AF: 0.00519

Gnomad4 EAS AF: 0.0575

Gnomad4 SAS AF: 0.0253

Gnomad4 FIN AF: 0.0101

Gnomad4 NFE AF: 0.00632

Gnomad4 OTH AF: 0.0161

Alfa AF: 0.00942 Hom.: 1

Bravo AF: 0.0170

Asia WGS AF: 0.0460 AC: 161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.5
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10501861; hg19: chr11-96470737;