rs2125511

Variant names:

• chr8-109228745-T-A
• rs2125511

Your query was ambiguous. Multiple possible variants found:

• chr8-109228745-T-A
• chr8-109228745-T-C
• chr8-109228745-T-G

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 0.638 in 152,126 control chromosomes in the GnomAD database, including 32,421 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 0.64 (32421 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0200

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.839 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: 0.637 AC: 96896 AN: 152008 Hom.: 32368 Cov.: 33

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.702

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.638 AC: 97011 AN: 152126 Hom.: 32421 Cov.: 33 AF XY: 0.637 AC XY: 47332 AN XY: 74330

Gnomad4 AFR AF: 0.846

Gnomad4 AMR AF: 0.656

Gnomad4 ASJ AF: 0.403

Gnomad4 EAS AF: 0.528

Gnomad4 SAS AF: 0.668

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.542

Gnomad4 OTH AF: 0.626

Alfa AF: 0.470 Hom.: 1374

Bravo AF: 0.653

Asia WGS AF: 0.658 AC: 2289 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.2
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2125511; hg19: chr8-110240974;