rs2455280

Positions:

• chr5-36460323-T-C
• chr5-36460323-T-G

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 0.0809 in 152,226 control chromosomes in the GnomAD database, including 551 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 0.081 (551 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.76

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0809 AC: 12302 AN: 152108 Hom.: 547 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0703

Gnomad ASJ AF: 0.0697

Gnomad EAS AF: 0.0626

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.0546

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0636

Gnomad OTH AF: 0.0933

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

GnomAD4 genome AF: 0.0809 AC: 12320 AN: 152226 Hom.: 551 Cov.: 32 AF XY: 0.0820 AC XY: 6104 AN XY: 74436

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.0702

Gnomad4 ASJ AF: 0.0697

Gnomad4 EAS AF: 0.0628

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.0546

Gnomad4 NFE AF: 0.0636

Gnomad4 OTH AF: 0.0923

Alfa AF: 0.0651 Hom.: 435

Bravo AF: 0.0799

Asia WGS AF: 0.133 AC: 462 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.11
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2455280; hg19: chr5-36460425;