rs2069852

Variant names:

• chr7-22732641-G-A
• rs2069852

Your query was ambiguous. Multiple possible variants found:

• chr7-22732641-G-A
• chr7-22732641-G-C

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 0.0854 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
• Publications: 25 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0748 AC: 3066 AN: 40962

American (AMR) AF: 0.160 AC: 2400 AN: 15016

Ashkenazi Jewish (ASJ) AF: 0.0297 AC: 103 AN: 3472

East Asian (EAS) AF: 0.673 AC: 3380 AN: 5024

South Asian (SAS) AF: 0.277 AC: 1328 AN: 4786

European-Finnish (FIN) AF: 0.0197 AC: 204 AN: 10336

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0319 AC: 2164 AN: 67824

Other (OTH) AF: 0.0852 AC: 178 AN: 2090

Alfa AF: 0.0634 Hom.: 2064

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
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs2069852; hg19: chr7-22772260;