11-27816489-A-G

Variant names:

• chr11-27816489-A-G
• rs10501088
• ENST00000530663.1:n.147+61013T>C

Variant summary

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

The ENST00000530663.1(ENSG00000255496):​n.147+61013T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.829 in 152,132 control chromosomes in the GnomAD database, including 52,570 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 0.83 (52570 hom., cov: 31)
• Consequence: ENSG00000255496 ENST00000530663.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160
• Publications: 1 publications found

Genes affected

ENSG00000255496 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.846 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
ENSG00000255496	ENST00000530663.1	n.147+61013T>C		intron_variant	Intron 1 of 1	1

Frequencies

GnomAD3 genomes AF: 0.829 AC: 126057 AN: 152014 Hom.: 52529 Cov.: 31

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.889

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.937

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.851

Gnomad OTH AF: 0.852

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

GnomAD4 genome AF: 0.829 AC: 126146 AN: 152132 Hom.: 52570 Cov.: 31 AF XY: 0.830 AC XY: 61768 AN XY: 74380

African (AFR) AF: 0.800 AC: 33187 AN: 41466

American (AMR) AF: 0.793 AC: 12118 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.889 AC: 3086 AN: 3472

East Asian (EAS) AF: 0.669 AC: 3464 AN: 5178

South Asian (SAS) AF: 0.758 AC: 3651 AN: 4816

European-Finnish (FIN) AF: 0.937 AC: 9928 AN: 10596

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.851 AC: 57895 AN: 68002

Other (OTH) AF: 0.852 AC: 1797 AN: 2110

Alfa AF: 0.841 Hom.: 7940

Bravo AF: 0.819

Asia WGS AF: 0.745 AC: 2594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.0
DANN	Benign	0.73
PhyloP100		-0.016

Splicing

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

Other links and lift over

dbSNP: rs10501088; hg19: chr11-27838036;