rs2025488

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;