rs1824777

Variant names:

• chr5-100278897-G-T
• rs1824777

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 0.363 in 151,998 control chromosomes in the GnomAD database, including 11,183 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 0.36 (11183 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.515 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: 0.363 AC: 55169 AN: 151880 Hom.: 11160 Cov.: 32

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.0201

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.363 AC: 55241 AN: 151998 Hom.: 11183 Cov.: 32 AF XY: 0.356 AC XY: 26471 AN XY: 74286

Gnomad4 AFR AF: 0.521

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.0201

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.381

Alfa AF: 0.341 Hom.: 5903

Bravo AF: 0.386

Asia WGS AF: 0.106 AC: 372 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.075
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1824777; hg19: chr5-99614601;