rs2732549

Positions:

• chr11-35066852-G-A
• chr11-35066852-G-C

Variant summary

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

The ENST00000685560.1(ENSG00000289526):​n.72C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 151,830 control chromosomes in the GnomAD database, including 37,021 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 0.68 (37021 hom., cov: 30)
• Consequence: ENSG00000289526 ENST00000685560.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.791

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 (AFR) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376626	XR_001748180.2	n.340C>T		non_coding_transcript_exon_variant	1/4
LOC105376626	XR_007062653.1	n.340C>T		non_coding_transcript_exon_variant	1/5
LOC105376626	XR_007062654.1	n.340C>T		non_coding_transcript_exon_variant	1/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000289526	ENST00000685560.1	n.72C>T		non_coding_transcript_exon_variant	1/3
ENSG00000289526	ENST00000687081.1	n.341C>T		non_coding_transcript_exon_variant	1/2
ENSG00000289526	ENST00000701115.1	n.52C>T		non_coding_transcript_exon_variant	1/3
ENSG00000289526	ENST00000702237.1	n.52C>T		non_coding_transcript_exon_variant	1/3

Frequencies

GnomAD3 genomes AF: 0.681 AC: 103343 AN: 151712 Hom.: 36964 Cov.: 30

Gnomad AFR AF: 0.905

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.791

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.681 AC: 103453 AN: 151830 Hom.: 37021 Cov.: 30 AF XY: 0.684 AC XY: 50716 AN XY: 74166

Gnomad4 AFR AF: 0.906

Gnomad4 AMR AF: 0.669

Gnomad4 ASJ AF: 0.636

Gnomad4 EAS AF: 0.791

Gnomad4 SAS AF: 0.779

Gnomad4 FIN AF: 0.538

Gnomad4 NFE AF: 0.558

Gnomad4 OTH AF: 0.682

Alfa AF: 0.579 Hom.: 23171

Bravo AF: 0.697

Asia WGS AF: 0.777 AC: 2704 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	7.6
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2732549; hg19: chr11-35088399;