chr7-46206982-A-G

Variant names:

• chr7-46206982-A-G
• rs9691259

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;