rs289034

Positions:

• chr5-114786468-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;