11-35063045-T-C

Position:

• chr11-35063045-T-C

Variant summary

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

The ENST00000685560.1(ENSG00000289526):​n.437+2075A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 152,026 control chromosomes in the GnomAD database, including 21,246 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 0.52 (21246 hom., cov: 32)
• Consequence: ENSG00000289526 ENST00000685560.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190

Genes affected

ENSG00000289526 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376626	XR_001748180.2	n.705+2075A>G		intron_variant
LOC105376626	XR_007062653.1	n.705+2075A>G		intron_variant
LOC105376626	XR_007062654.1	n.705+2075A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000289526	ENST00000685560.1	n.437+2075A>G		intron_variant
ENSG00000289526	ENST00000701115.1	n.417+2075A>G		intron_variant
ENSG00000289526	ENST00000702237.1	n.223+3636A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78464 AN: 151910 Hom.: 21241 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.516 AC: 78482 AN: 152026 Hom.: 21246 Cov.: 32 AF XY: 0.521 AC XY: 38733 AN XY: 74316

Gnomad4 AFR AF: 0.352

Gnomad4 AMR AF: 0.607

Gnomad4 ASJ AF: 0.614

Gnomad4 EAS AF: 0.753

Gnomad4 SAS AF: 0.690

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.558

Gnomad4 OTH AF: 0.551

Alfa AF: 0.559 Hom.: 40396

Bravo AF: 0.513

Asia WGS AF: 0.687 AC: 2390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.3
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2732552; hg19: chr11-35084592;