5-34551654-C-T

Position:

• chr5-34551654-C-T

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 0.691 in 152,084 control chromosomes in the GnomAD database, including 36,913 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 0.69 (36913 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.815

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.759 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

Frequencies

GnomAD3 genomes AF: 0.691 AC: 105075 AN: 151966 Hom.: 36908 Cov.: 33

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.760

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.792

Gnomad EAS AF: 0.660

Gnomad SAS AF: 0.597

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.706

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

GnomAD4 genome AF: 0.691 AC: 105110 AN: 152084 Hom.: 36913 Cov.: 33 AF XY: 0.685 AC XY: 50897 AN XY: 74334

Gnomad4 AFR AF: 0.565

Gnomad4 AMR AF: 0.737

Gnomad4 ASJ AF: 0.792

Gnomad4 EAS AF: 0.660

Gnomad4 SAS AF: 0.597

Gnomad4 FIN AF: 0.661

Gnomad4 NFE AF: 0.765

Gnomad4 OTH AF: 0.701

Alfa AF: 0.711 Hom.: 4836

Bravo AF: 0.695

Asia WGS AF: 0.611 AC: 2130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.9
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6866893; hg19: chr5-34551759;