rs701992

Variant names:

• chr3-120603552-A-T
• rs701992

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 0.238 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
• Publications: 1 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 (AFR) allele frequency at 95% confidence interval = 0.429 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: 0.238 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

African (AFR) AF: 0.435 AC: 18018 AN: 41458

American (AMR) AF: 0.152 AC: 2325 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 527 AN: 3470

East Asian (EAS) AF: 0.0309 AC: 160 AN: 5182

South Asian (SAS) AF: 0.185 AC: 891 AN: 4824

European-Finnish (FIN) AF: 0.109 AC: 1160 AN: 10604

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12470 AN: 67986

Other (OTH) AF: 0.217 AC: 458 AN: 2114

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
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs701992; hg19: chr3-120322399;