rs4294125

chr7-94154081-G-A

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/exons	MANE	UniProt

Ensembl

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