rs1876525

Variant names:

• chr6-86442374-C-G
• rs1876525

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 0.0702 in 152,214 control chromosomes in the GnomAD database, including 493 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 0.070 (493 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.128 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: 0.0702 AC: 10682 AN: 152096 Hom.: 494 Cov.: 32

Gnomad AFR AF: 0.0261

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.0818

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.0349

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.0744

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0866

Gnomad OTH AF: 0.0933

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

GnomAD4 genome AF: 0.0702 AC: 10686 AN: 152214 Hom.: 493 Cov.: 32 AF XY: 0.0710 AC XY: 5281 AN XY: 74422

Gnomad4 AFR AF: 0.0263

Gnomad4 AMR AF: 0.0816

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.0349

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.0744

Gnomad4 NFE AF: 0.0866

Gnomad4 OTH AF: 0.0909

Alfa AF: 0.0705 Hom.: 52

Bravo AF: 0.0665

Asia WGS AF: 0.0860 AC: 298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.0
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1876525; hg19: chr6-87152092;