rs289034

Variant names:

• chr5-114786468-T-C
• rs289034

Variant summary

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

The variant allele was found at a frequency of 0.675 in 152,076 control chromosomes in the GnomAD database, including 35,106 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 (35106 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131

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 = 0.776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.675 AC: 102604 AN: 151958 Hom.: 35050 Cov.: 33

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.597

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.675 AC: 102719 AN: 152076 Hom.: 35106 Cov.: 33 AF XY: 0.669 AC XY: 49735 AN XY: 74338

Gnomad4 AFR AF: 0.783

Gnomad4 AMR AF: 0.668

Gnomad4 ASJ AF: 0.663

Gnomad4 EAS AF: 0.746

Gnomad4 SAS AF: 0.597

Gnomad4 FIN AF: 0.571

Gnomad4 NFE AF: 0.629

Gnomad4 OTH AF: 0.675

Alfa AF: 0.636 Hom.: 15112

Bravo AF: 0.688

Asia WGS AF: 0.697 AC: 2423 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	1.1
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs289034; hg19: chr5-114122165; COSMIC: COSV50462993;