rs1862326

Variant names:

• chr5-180366256-G-T
• rs1862326

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 0.208 in 152,168 control chromosomes in the GnomAD database, including 3,688 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 0.21 (3688 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.567

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.362 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: 0.208 AC: 31620 AN: 152050 Hom.: 3676 Cov.: 33

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.208 AC: 31677 AN: 152168 Hom.: 3688 Cov.: 33 AF XY: 0.210 AC XY: 15640 AN XY: 74388

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.376

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.207

Alfa AF: 0.165 Hom.: 4819

Bravo AF: 0.210

Asia WGS AF: 0.340 AC: 1181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.68
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1862326; hg19: chr5-179793256;