rs289847

chr2-151169371-C-A

Variant summary

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

The ENST00000652733.1(ENSG00000236885):n.69+16749G>T 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 0.579 in 151,972 control chromosomes in the GnomAD database, including 27,179 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 0.58 (27179 hom., cov: 32)
• Consequence: ENST00000652733.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800

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 (AFR) allele frequency at 95% confidence interval = 0.794 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
	ENST00000652733.1	n.69+16749G>T		intron_variant, non_coding_transcript_variant
	ENST00000447078.1	n.90+16749G>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87847 AN: 151854 Hom.: 27122 Cov.: 32

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.579 AC: 87956 AN: 151972 Hom.: 27179 Cov.: 32 AF XY: 0.576 AC XY: 42740 AN XY: 74238

Gnomad4 AFR AF: 0.801

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.594

Gnomad4 EAS AF: 0.467

Gnomad4 SAS AF: 0.676

Gnomad4 FIN AF: 0.399

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.589

Alfa AF: 0.544 Hom.: 2864

Bravo AF: 0.586

Asia WGS AF: 0.594 AC: 2062 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	0.66
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs289847; hg19: chr2-152025885;