rs4529888

chr11-127211696-G-Achr11-127211696-G-C

Variant summary

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

The ENST00000609845.1(ENSG00000272642):n.306-11536G>A 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 0.679 in 152,068 control chromosomes in the GnomAD database, including 36,042 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 (36042 hom., cov: 32)
• Consequence: ENST00000609845.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.487

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.92 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
	ENST00000609845.1	n.306-11536G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.679 AC: 103196 AN: 151950 Hom.: 35989 Cov.: 32

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.942

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.679 AC: 103311 AN: 152068 Hom.: 36042 Cov.: 32 AF XY: 0.685 AC XY: 50927 AN XY: 74316

Gnomad4 AFR AF: 0.798

Gnomad4 AMR AF: 0.707

Gnomad4 ASJ AF: 0.571

Gnomad4 EAS AF: 0.942

Gnomad4 SAS AF: 0.716

Gnomad4 FIN AF: 0.675

Gnomad4 NFE AF: 0.586

Gnomad4 OTH AF: 0.627

Alfa AF: 0.598 Hom.: 32749

Bravo AF: 0.689

Asia WGS AF: 0.857 AC: 2978 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.0
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4529888; hg19: chr11-127081591;