rs1455280

Variant names:

• chr4-60905713-A-G
• rs1455280

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 0.11 in 152,108 control chromosomes in the GnomAD database, including 1,046 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 0.11 (1046 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.773

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.134 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: 0.110 AC: 16777 AN: 151990 Hom.: 1043 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.0890

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.0158

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.0640

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.110 AC: 16798 AN: 152108 Hom.: 1046 Cov.: 32 AF XY: 0.108 AC XY: 8028 AN XY: 74360

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.0889

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.0159

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.0640

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.127

Alfa AF: 0.121 Hom.: 1633

Bravo AF: 0.112

Asia WGS AF: 0.0920 AC: 321 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.6
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1455280; hg19: chr4-61771431;