rs854572

chr7-95325384-C-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 0.41 in 152,048 control chromosomes in the GnomAD database, including 14,889 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 0.41 (14889 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.317

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.526 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: 0.410 AC: 62298 AN: 151930 Hom.: 14893 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.410 AC: 62305 AN: 152048 Hom.: 14889 Cov.: 32 AF XY: 0.407 AC XY: 30237 AN XY: 74314

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.445

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.531

Gnomad4 OTH AF: 0.485

Alfa AF: 0.447 Hom.: 2072

Bravo AF: 0.412

Asia WGS AF: 0.404 AC: 1408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	2.3
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs854572; hg19: chr7-94954696;