rs4294125

Variant names:

• chr7-94154081-G-A
• rs4294125

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 0.0269 in 151,842 control chromosomes in the GnomAD database, including 126 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 0.027 (126 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0815 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: 0.0268 AC: 4069 AN: 151724 Hom.: 126 Cov.: 32

Gnomad AFR AF: 0.0396

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0720

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0882

Gnomad SAS AF: 0.0388

Gnomad FIN AF: 0.00473

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00867

Gnomad OTH AF: 0.0250

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

GnomAD4 genome AF: 0.0269 AC: 4082 AN: 151842 Hom.: 126 Cov.: 32 AF XY: 0.0275 AC XY: 2042 AN XY: 74214

Gnomad4 AFR AF: 0.0398

Gnomad4 AMR AF: 0.0722

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.0882

Gnomad4 SAS AF: 0.0387

Gnomad4 FIN AF: 0.00473

Gnomad4 NFE AF: 0.00867

Gnomad4 OTH AF: 0.0252

Alfa AF: 0.0206 Hom.: 8

Bravo AF: 0.0326

Asia WGS AF: 0.0530 AC: 186 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.8
DANN	Benign	0.96

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4294125; hg19: chr7-93783393;