rs6873221

Variant names:

• chr5-25928457-G-A
• rs6873221

Your query was ambiguous. Multiple possible variants found:

• chr5-25928457-G-A
• chr5-25928457-G-C
• chr5-25928457-G-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 0.467 in 151,678 control chromosomes in the GnomAD database, including 16,688 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 0.47 (16688 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.354
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.576 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: 0.467 AC: 70722 AN: 151558 Hom.: 16673 Cov.: 32

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.428

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.467 AC: 70781 AN: 151678 Hom.: 16688 Cov.: 32 AF XY: 0.468 AC XY: 34704 AN XY: 74114

African (AFR) AF: 0.521 AC: 21575 AN: 41402

American (AMR) AF: 0.440 AC: 6700 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.377 AC: 1308 AN: 3472

East Asian (EAS) AF: 0.594 AC: 3062 AN: 5158

South Asian (SAS) AF: 0.511 AC: 2464 AN: 4818

European-Finnish (FIN) AF: 0.432 AC: 4545 AN: 10518

Middle Eastern (MID) AF: 0.423 AC: 121 AN: 286

European-Non Finnish (NFE) AF: 0.439 AC: 29744 AN: 67778

Other (OTH) AF: 0.448 AC: 945 AN: 2108

Alfa AF: 0.455 Hom.: 2634

Bravo AF: 0.466

Asia WGS AF: 0.554 AC: 1904 AN: 3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.3
DANN	Benign	0.25
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs6873221; hg19: chr5-25928566;