rs822552

Positions:

• chr7-148953542-C-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 0.292 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;