rs1824935

Variant names:

• chr5-154606753-G-C
• rs1824935

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 0.352 in 151,998 control chromosomes in the GnomAD database, including 9,813 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 0.35 (9813 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.707

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.386 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: 0.353 AC: 53546 AN: 151880 Hom.: 9812 Cov.: 32

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.352 AC: 53560 AN: 151998 Hom.: 9813 Cov.: 32 AF XY: 0.353 AC XY: 26207 AN XY: 74268

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.358

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.392

Alfa AF: 0.369 Hom.: 1328

Bravo AF: 0.335

Asia WGS AF: 0.366 AC: 1273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.54
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: rs1824935; hg19: chr5-153986313;