rs701992

chr3-120603552-A-T

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 0.238 in 152,128 control chromosomes in the GnomAD database, including 5,499 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 0.24 (5499 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.429 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: 0.238 AC: 36233 AN: 152010 Hom.: 5491 Cov.: 32

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.0308

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.238 AC: 36272 AN: 152128 Hom.: 5499 Cov.: 32 AF XY: 0.229 AC XY: 16998 AN XY: 74386

Gnomad4 AFR AF: 0.435

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.0309

Gnomad4 SAS AF: 0.185

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.217

Alfa AF: 0.210 Hom.: 510

Bravo AF: 0.249

Asia WGS AF: 0.120 AC: 420 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	0.55
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs701992; hg19: chr3-120322399;