rs2108225

Variant names:

• chr7-107812658-G-A
• rs2108225

Your query was ambiguous. Multiple possible variants found:

• chr7-107812658-G-A
• chr7-107812658-G-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 0.549 in 151,520 control chromosomes in the GnomAD database, including 24,937 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 0.55 (24937 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.527

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 (AFR) allele frequency at 95% confidence interval = 0.796 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: 0.549 AC: 83149 AN: 151412 Hom.: 24889 Cov.: 30

Gnomad AFR AF: 0.803

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.549 AC: 83259 AN: 151520 Hom.: 24937 Cov.: 30 AF XY: 0.548 AC XY: 40584 AN XY: 74010

Gnomad4 AFR AF: 0.803

Gnomad4 AMR AF: 0.488

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.400

Gnomad4 SAS AF: 0.533

Gnomad4 FIN AF: 0.506

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.532

Alfa AF: 0.450 Hom.: 34972

Bravo AF: 0.560

Asia WGS AF: 0.499 AC: 1727 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.9
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: rs2108225; hg19: chr7-107453103;