rs1560326

chr5-97691782-A-Gchr5-97691782-A-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 0.0832 in 152,100 control chromosomes in the GnomAD database, including 1,063 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 0.083 (1063 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.211 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: 0.0829 AC: 12601 AN: 151982 Hom.: 1058 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0533

Gnomad ASJ AF: 0.0337

Gnomad EAS AF: 0.0906

Gnomad SAS AF: 0.0286

Gnomad FIN AF: 0.0437

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0234

Gnomad OTH AF: 0.0685

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

GnomAD4 genome AF: 0.0832 AC: 12651 AN: 152100 Hom.: 1063 Cov.: 32 AF XY: 0.0820 AC XY: 6101 AN XY: 74370

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.0532

Gnomad4 ASJ AF: 0.0337

Gnomad4 EAS AF: 0.0905

Gnomad4 SAS AF: 0.0284

Gnomad4 FIN AF: 0.0437

Gnomad4 NFE AF: 0.0234

Gnomad4 OTH AF: 0.0697

Alfa AF: 0.0372 Hom.: 123

Bravo AF: 0.0915

Asia WGS AF: 0.0700 AC: 244 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.017
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1560326; hg19: chr5-97027486;