11-45506566-T-G

Position:

• chr11-45506566-T-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000254746 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC105376654	XR_001748204.3	n.712-16795A>C		intron_variant
LOC105376654	XR_931245.4	n.369-16795A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000254746	ENST00000527642.5	n.496-16795A>C		intron_variant		4
ENSG00000255041	ENST00000528445.1	n.530+6707A>C		intron_variant		5
ENSG00000254746	ENST00000533315.5	n.491-16795A>C		intron_variant		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

Gnomad4 AFR AF: 0.732

Gnomad4 AMR AF: 0.871

Gnomad4 ASJ AF: 0.829

Gnomad4 EAS AF: 0.871

Gnomad4 SAS AF: 0.889

Gnomad4 FIN AF: 0.824

Gnomad4 NFE AF: 0.838

Gnomad4 OTH AF: 0.810

Alfa AF: 0.832 Hom.: 105042

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1488665; hg19: chr11-45528116;