rs6969923

Positions:

• chr7-106926914-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 0.42 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.388

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.448

Gnomad4 SAS AF: 0.425

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.446

Gnomad4 OTH AF: 0.428

Alfa AF: 0.437 Hom.: 2012

Bravo AF: 0.413

Asia WGS AF: 0.437 AC: 1520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6969923; hg19: chr7-106567359;