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. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0763 AC: 3169 AN: 41560

American (AMR) AF: 0.131 AC: 2007 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0917 AC: 318 AN: 3468

East Asian (EAS) AF: 0.135 AC: 697 AN: 5182

South Asian (SAS) AF: 0.149 AC: 718 AN: 4828

European-Finnish (FIN) AF: 0.0486 AC: 516 AN: 10620

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0648 AC: 4405 AN: 68026

Other (OTH) AF: 0.101 AC: 212 AN: 2108

Alfa AF: 0.0708 Hom.: 724

Bravo AF: 0.0858

Asia WGS AF: 0.171 AC: 593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.39
DANN	Benign	0.26
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs6881280; hg19: chr5-122615524;