rs1363688

Variant names:

• chr5-175182728-G-A
• rs1363688

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.406 AC: 16811 AN: 41450

American (AMR) AF: 0.267 AC: 4079 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 717 AN: 3468

East Asian (EAS) AF: 0.270 AC: 1397 AN: 5170

South Asian (SAS) AF: 0.236 AC: 1137 AN: 4814

European-Finnish (FIN) AF: 0.195 AC: 2063 AN: 10584

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12720 AN: 68000

Other (OTH) AF: 0.286 AC: 605 AN: 2114

Alfa AF: 0.213 Hom.: 2634

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
PhyloP100		-0.029

Splicing

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

Other links and lift over

dbSNP: rs1363688; hg19: chr5-174609731;