rs1363688

Positions:

• chr5-175182728-G-A

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 0.262 in 152,092 control chromosomes in the GnomAD database, including 5,924 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 0.26 (5924 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.4 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: 0.262 AC: 39761 AN: 151974 Hom.: 5913 Cov.: 32

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.262 AC: 39807 AN: 152092 Hom.: 5924 Cov.: 32 AF XY: 0.261 AC XY: 19405 AN XY: 74346

Gnomad4 AFR AF: 0.406

Gnomad4 AMR AF: 0.267

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.286

Alfa AF: 0.210 Hom.: 2055

Bravo AF: 0.270

Asia WGS AF: 0.301 AC: 1047 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1363688; hg19: chr5-174609731;