rs822552

Variant names:

• chr7-148953542-C-G
• rs822552

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 0.292 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.292 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

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.290

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs822552; hg19: chr7-148650634;