rs7857628

chr9-6409874-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 0.348 in 152,028 control chromosomes in the GnomAD database, including 9,541 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 0.35 (9541 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73

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 (NFE) allele frequency at 95% confidence interval = 0.377 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: 0.348 AC: 52930 AN: 151910 Hom.: 9538 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.348 AC: 52945 AN: 152028 Hom.: 9541 Cov.: 32 AF XY: 0.352 AC XY: 26185 AN XY: 74304

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.375

Gnomad4 ASJ AF: 0.401

Gnomad4 EAS AF: 0.278

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.381

Gnomad4 OTH AF: 0.365

Alfa AF: 0.369 Hom.: 6084

Bravo AF: 0.340

Asia WGS AF: 0.269 AC: 937 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.52
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7857628; hg19: chr9-6409874;