rs1991384

Variant names:

• chr3-69707224-T-A
• rs1991384

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 0.0362 in 152,290 control chromosomes in the GnomAD database, including 233 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 0.036 (233 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.396
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0362 AC: 5504 AN: 152172 Hom.: 229 Cov.: 32

Gnomad AFR AF: 0.0304

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0325

Gnomad EAS AF: 0.0772

Gnomad SAS AF: 0.0788

Gnomad FIN AF: 0.00838

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0209

Gnomad OTH AF: 0.0325

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

GnomAD4 genome AF: 0.0362 AC: 5512 AN: 152290 Hom.: 233 Cov.: 32 AF XY: 0.0372 AC XY: 2769 AN XY: 74464

African (AFR) AF: 0.0302 AC: 1257 AN: 41558

American (AMR) AF: 0.116 AC: 1779 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0325 AC: 113 AN: 3472

East Asian (EAS) AF: 0.0772 AC: 400 AN: 5180

South Asian (SAS) AF: 0.0785 AC: 379 AN: 4828

European-Finnish (FIN) AF: 0.00838 AC: 89 AN: 10618

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0209 AC: 1419 AN: 68020

Other (OTH) AF: 0.0331 AC: 70 AN: 2114

Alfa AF: 0.0312 Hom.: 24

Bravo AF: 0.0436

Asia WGS AF: 0.101 AC: 349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.0
DANN	Benign	0.71
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs1991384; hg19: chr3-69756375;