rs952151

chr11-121787804-A-Gchr11-121787804-A-T

Variant summary

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

The ENST00000652518.1(ENSG00000286044):n.140-81518A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.651 in 152,126 control chromosomes in the GnomAD database, including 34,655 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 0.65 (34655 hom., cov: 33)
• Consequence: ENST00000652518.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.562

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000652518.1	n.140-81518A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.652 AC: 99037 AN: 152008 Hom.: 34647 Cov.: 33

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.758

Gnomad EAS AF: 0.871

Gnomad SAS AF: 0.771

Gnomad FIN AF: 0.765

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.651 AC: 99079 AN: 152126 Hom.: 34655 Cov.: 33 AF XY: 0.657 AC XY: 48892 AN XY: 74386

Gnomad4 AFR AF: 0.368

Gnomad4 AMR AF: 0.715

Gnomad4 ASJ AF: 0.758

Gnomad4 EAS AF: 0.872

Gnomad4 SAS AF: 0.770

Gnomad4 FIN AF: 0.765

Gnomad4 NFE AF: 0.760

Gnomad4 OTH AF: 0.671

Alfa AF: 0.621 Hom.: 4368

Bravo AF: 0.635

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.54
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs952151; hg19: chr11-121658512;