rs6969923

Variant names:

• chr7-106926914-A-G
• rs6969923

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 0.42 in 152,018 control chromosomes in the GnomAD database, including 13,544 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 0.42 (13544 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.442 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: 0.420 AC: 63829 AN: 151900 Hom.: 13536 Cov.: 32

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.420 AC: 63874 AN: 152018 Hom.: 13544 Cov.: 32 AF XY: 0.420 AC XY: 31244 AN XY: 74318

African (AFR) AF: 0.380 AC: 15761 AN: 41478

American (AMR) AF: 0.388 AC: 5911 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1422 AN: 3468

East Asian (EAS) AF: 0.448 AC: 2315 AN: 5172

South Asian (SAS) AF: 0.425 AC: 2047 AN: 4814

European-Finnish (FIN) AF: 0.451 AC: 4766 AN: 10570

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.446 AC: 30296 AN: 67958

Other (OTH) AF: 0.428 AC: 903 AN: 2112

Alfa AF: 0.434 Hom.: 2063

Bravo AF: 0.413

Asia WGS AF: 0.437 AC: 1520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	11
DANN	Benign	0.83
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs6969923; hg19: chr7-106567359;