rs2455280

Variant names:

• chr5-36460323-T-C
• rs2455280

Your query was ambiguous. Multiple possible variants found:

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

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 0.0809 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
• Publications: 5 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.114 AC: 4749 AN: 41532

American (AMR) AF: 0.0702 AC: 1074 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0697 AC: 241 AN: 3458

East Asian (EAS) AF: 0.0628 AC: 325 AN: 5178

South Asian (SAS) AF: 0.165 AC: 793 AN: 4820

European-Finnish (FIN) AF: 0.0546 AC: 579 AN: 10608

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0636 AC: 4324 AN: 68022

Other (OTH) AF: 0.0923 AC: 195 AN: 2112

Alfa AF: 0.0663 Hom.: 569

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
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs2455280; hg19: chr5-36460425;