rs1363281

Variant names:

• chr5-170820294-G-A
• rs1363281

Your query was ambiguous. Multiple possible variants found:

• chr5-170820294-G-A
• chr5-170820294-G-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.428 in 152,034 control chromosomes in the GnomAD database, including 15,789 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 0.43 (15789 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.694 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: 0.428 AC: 64993 AN: 151916 Hom.: 15779 Cov.: 33

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.428 AC: 65010 AN: 152034 Hom.: 15789 Cov.: 33 AF XY: 0.434 AC XY: 32252 AN XY: 74328

African (AFR) AF: 0.199 AC: 8272 AN: 41474

American (AMR) AF: 0.533 AC: 8155 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1835 AN: 3470

East Asian (EAS) AF: 0.713 AC: 3678 AN: 5160

South Asian (SAS) AF: 0.671 AC: 3233 AN: 4818

European-Finnish (FIN) AF: 0.441 AC: 4648 AN: 10544

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.491 AC: 33401 AN: 67968

Other (OTH) AF: 0.472 AC: 996 AN: 2108

Alfa AF: 0.457 Hom.: 8606

Bravo AF: 0.422

Asia WGS AF: 0.635 AC: 2209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	17
DANN	Benign	0.48
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs1363281; hg19: chr5-170247298;