rs6881280

Variant names:

• chr5-123279830-A-G
• rs6881280

Your query was ambiguous. Multiple possible variants found:

• chr5-123279830-A-G
• chr5-123279830-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 0.0796 in 152,304 control chromosomes in the GnomAD database, including 545 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 0.080 (545 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.694

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.14 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: 0.0797 AC: 12123 AN: 152186 Hom.: 544 Cov.: 33

Gnomad AFR AF: 0.0765

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.0917

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.0486

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0648

Gnomad OTH AF: 0.0968

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

GnomAD4 genome AF: 0.0796 AC: 12129 AN: 152304 Hom.: 545 Cov.: 33 AF XY: 0.0811 AC XY: 6043 AN XY: 74476

Gnomad4 AFR AF: 0.0763

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.0917

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.0486

Gnomad4 NFE AF: 0.0648

Gnomad4 OTH AF: 0.101

Alfa AF: 0.0742 Hom.: 143

Bravo AF: 0.0858

Asia WGS AF: 0.171 AC: 593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.39
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6881280; hg19: chr5-122615524;