rs7857628

Variant names:

• chr9-6409874-A-G
• rs7857628

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;