rs789254

Positions:

• chr3-128855750-C-T

Variant summary

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

The ENST00000703686.1(ENSG00000290242):​n.489G>A 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 0.554 in 152,100 control chromosomes in the GnomAD database, including 26,426 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 0.55 (26426 hom., cov: 32)
• Consequence: ENST00000703686.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.702 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000703686.1	n.489G>A		non_coding_transcript_exon_variant	2/2
	ENST00000703685.1	n.437+4774C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84217 AN: 151982 Hom.: 26423 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.554 AC: 84241 AN: 152100 Hom.: 26426 Cov.: 32 AF XY: 0.558 AC XY: 41499 AN XY: 74368

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.596

Gnomad4 ASJ AF: 0.599

Gnomad4 EAS AF: 0.385

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.725

Gnomad4 NFE AF: 0.707

Gnomad4 OTH AF: 0.569

Alfa AF: 0.623 Hom.: 5334

Bravo AF: 0.529

Asia WGS AF: 0.523 AC: 1817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.1
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs789254; hg19: chr3-128574593;