rs2069852

chr7-22732641-G-Achr7-22732641-G-C

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 0.0854 in 150,704 control chromosomes in the GnomAD database, including 1,736 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 0.085 (1736 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.375

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.654 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: 0.0853 AC: 12846 AN: 150592 Hom.: 1740 Cov.: 30

Gnomad AFR AF: 0.0747

Gnomad AMI AF: 0.0444

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.0197

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0319

Gnomad OTH AF: 0.0832

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

GnomAD4 genome AF: 0.0854 AC: 12868 AN: 150704 Hom.: 1736 Cov.: 30 AF XY: 0.0918 AC XY: 6747 AN XY: 73504

Gnomad4 AFR AF: 0.0748

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.0297

Gnomad4 EAS AF: 0.673

Gnomad4 SAS AF: 0.277

Gnomad4 FIN AF: 0.0197

Gnomad4 NFE AF: 0.0319

Gnomad4 OTH AF: 0.0852

Alfa AF: 0.0593 Hom.: 168

Bravo AF: 0.0961

Asia WGS AF: 0.413 AC: 1437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	3.4
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2069852; hg19: chr7-22772260;