11-45506566-T-G

Variant names:

• chr11-45506566-T-G
• rs1488665
• ENST00000527642.5:n.496-16795A>C

Variant summary

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

The ENST00000527642.5(ENSG00000254746):​n.496-16795A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.813 in 152,212 control chromosomes in the GnomAD database, including 50,612 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 0.81 (50612 hom., cov: 34)
• Consequence: ENSG00000254746 ENST00000527642.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.948
• Publications: 6 publications found

Genes affected

ENSG00000254746 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376654	XR_001748204.3	n.712-16795A>C		intron_variant	Intron 4 of 4
LOC105376654	XR_931245.4	n.369-16795A>C		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254746	ENST00000527642.5	n.496-16795A>C		intron_variant	Intron 5 of 5	4
ENSG00000255041	ENST00000528445.1	n.530+6707A>C		intron_variant	Intron 1 of 2	5
ENSG00000254746	ENST00000533315.5	n.491-16795A>C		intron_variant	Intron 4 of 4	4

Frequencies

GnomAD3 genomes AF: 0.813 AC: 123698 AN: 152094 Hom.: 50580 Cov.: 34

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.871

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.871

Gnomad SAS AF: 0.889

Gnomad FIN AF: 0.824

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.809

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

GnomAD4 genome AF: 0.813 AC: 123782 AN: 152212 Hom.: 50612 Cov.: 34 AF XY: 0.814 AC XY: 60577 AN XY: 74420

African (AFR) AF: 0.732 AC: 30387 AN: 41514

American (AMR) AF: 0.871 AC: 13333 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.829 AC: 2877 AN: 3472

East Asian (EAS) AF: 0.871 AC: 4516 AN: 5184

South Asian (SAS) AF: 0.889 AC: 4298 AN: 4834

European-Finnish (FIN) AF: 0.824 AC: 8717 AN: 10580

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.838 AC: 56993 AN: 68004

Other (OTH) AF: 0.810 AC: 1713 AN: 2116

Alfa AF: 0.828 Hom.: 226450

Bravo AF: 0.812

Asia WGS AF: 0.883 AC: 3073 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.14
DANN	Benign	0.45
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs1488665; hg19: chr11-45528116;