7-46206982-A-G

Variant names:

• chr7-46206982-A-G
• rs9691259

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.360 AC: 14925 AN: 41476

American (AMR) AF: 0.211 AC: 3222 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 672 AN: 3470

East Asian (EAS) AF: 0.230 AC: 1190 AN: 5168

South Asian (SAS) AF: 0.0798 AC: 385 AN: 4824

European-Finnish (FIN) AF: 0.263 AC: 2779 AN: 10586

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.205 AC: 13912 AN: 67990

Other (OTH) AF: 0.225 AC: 474 AN: 2110

Alfa AF: 0.213 Hom.: 9208

Bravo AF: 0.252

Asia WGS AF: 0.173 AC: 604 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.9
DANN	Benign	0.72
PhyloP100		0.076

Splicing

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

Other links and lift over

dbSNP: rs9691259; hg19: chr7-46246580;