rs7857015

Positions:

• chr9-134919395-A-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 0.275 in 152,212 control chromosomes in the GnomAD database, including 6,289 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 0.27 (6289 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41851 AN: 152094 Hom.: 6291 Cov.: 33

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.275 AC: 41840 AN: 152212 Hom.: 6289 Cov.: 33 AF XY: 0.274 AC XY: 20356 AN XY: 74424

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.346

Gnomad4 OTH AF: 0.273

Alfa AF: 0.290 Hom.: 978

Bravo AF: 0.261

Asia WGS AF: 0.150 AC: 524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7857015; hg19: chr9-137811241;