rs2025488

Variant names:

• chr6-87104484-C-G
• rs2025488

Your query was ambiguous. Multiple possible variants found:

• chr6-87104484-C-G
• chr6-87104484-C-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 0.386 in 151,794 control chromosomes in the GnomAD database, including 11,642 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 0.39 (11642 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.222

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 = 0.504 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: 0.386 AC: 58515 AN: 151674 Hom.: 11629 Cov.: 31

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.386 AC: 58561 AN: 151794 Hom.: 11642 Cov.: 31 AF XY: 0.391 AC XY: 29013 AN XY: 74146

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.521

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.392

Alfa AF: 0.357 Hom.: 1201

Bravo AF: 0.395

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.83
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2025488; hg19: chr6-87814202;