5-154606484-C-T

Variant names:

• chr5-154606484-C-T
• rs1824936

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 0.389 in 151,940 control chromosomes in the GnomAD database, including 11,726 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 0.39 (11726 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.138

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.398 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: 0.389 AC: 59068 AN: 151822 Hom.: 11721 Cov.: 31

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.389 AC: 59096 AN: 151940 Hom.: 11726 Cov.: 31 AF XY: 0.389 AC XY: 28854 AN XY: 74256

Gnomad4 AFR AF: 0.404

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.380

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.466

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.416

Alfa AF: 0.387 Hom.: 24505

Bravo AF: 0.376

Asia WGS AF: 0.386 AC: 1341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1824936; hg19: chr5-153986044;