rs9691259

Positions:

• chr7-46206982-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 0.249 in 152,120 control chromosomes in the GnomAD database, including 5,213 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 0.25 (5213 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.355 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: 0.248 AC: 37759 AN: 152000 Hom.: 5205 Cov.: 33

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.0804

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.249 AC: 37806 AN: 152120 Hom.: 5213 Cov.: 33 AF XY: 0.248 AC XY: 18467 AN XY: 74374

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.230

Gnomad4 SAS AF: 0.0798

Gnomad4 FIN AF: 0.263

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.225

Alfa AF: 0.239 Hom.: 454

Bravo AF: 0.252

Asia WGS AF: 0.173 AC: 604 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.9
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9691259; hg19: chr7-46246580;