rs1824777

Positions:

• chr5-100278897-G-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 0.363 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;