rs822552

Variant names:

• chr7-148953542-C-G
• rs822552

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 0.292 in 151,800 control chromosomes in the GnomAD database, including 6,942 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 0.29 (6942 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144
• Publications: 27 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.395 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: 0.292 AC: 44319 AN: 151682 Hom.: 6937 Cov.: 31

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.292 AC: 44361 AN: 151800 Hom.: 6942 Cov.: 31 AF XY: 0.289 AC XY: 21410 AN XY: 74156

African (AFR) AF: 0.400 AC: 16541 AN: 41390

American (AMR) AF: 0.200 AC: 3051 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 826 AN: 3468

East Asian (EAS) AF: 0.209 AC: 1079 AN: 5172

South Asian (SAS) AF: 0.193 AC: 926 AN: 4788

European-Finnish (FIN) AF: 0.309 AC: 3244 AN: 10510

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17769 AN: 67914

Other (OTH) AF: 0.290 AC: 612 AN: 2110

Alfa AF: 0.266 Hom.: 3087

Bravo AF: 0.291

Asia WGS AF: 0.221 AC: 772 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.41
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs822552; hg19: chr7-148650634;