rs7633800

Variant names:

• chr3-122292818-G-A
• rs7633800

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 0.269 in 152,102 control chromosomes in the GnomAD database, including 6,303 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 0.27 (6303 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.202

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.348 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: 0.270 AC: 40981 AN: 151984 Hom.: 6308 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.00385

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.269 AC: 40967 AN: 152102 Hom.: 6303 Cov.: 32 AF XY: 0.267 AC XY: 19854 AN XY: 74342

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.260

Gnomad4 EAS AF: 0.00386

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.277

Alfa AF: 0.301 Hom.: 1305

Bravo AF: 0.252

Asia WGS AF: 0.0900 AC: 314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7633800; hg19: chr3-122011665;