chr3-122292879-C-G

Variant names:

• chr3-122292879-C-G
• rs7633667

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 0.269 in 152,126 control chromosomes in the GnomAD database, including 6,305 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 (6305 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• 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: 40983 AN: 152008 Hom.: 6310 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.00384

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.269 AC: 40968 AN: 152126 Hom.: 6305 Cov.: 32 AF XY: 0.267 AC XY: 19851 AN XY: 74378

African (AFR) AF: 0.163 AC: 6750 AN: 41504

American (AMR) AF: 0.222 AC: 3402 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 910 AN: 3470

East Asian (EAS) AF: 0.00385 AC: 20 AN: 5192

South Asian (SAS) AF: 0.209 AC: 1008 AN: 4814

European-Finnish (FIN) AF: 0.377 AC: 3981 AN: 10556

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

European-Non Finnish (NFE) AF: 0.352 AC: 23896 AN: 67982

Other (OTH) AF: 0.277 AC: 585 AN: 2110

Alfa AF: 0.311 Hom.: 1013

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	-0.86
CADD	Benign	7.8
DANN	Benign	0.53
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs7633667; hg19: chr3-122011726;