rs1392705

Variant names:

• chr3-193815412-A-G
• rs1392705

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 0.298 in 151,838 control chromosomes in the GnomAD database, including 7,833 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 0.30 (7833 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.483 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: 0.298 AC: 45224 AN: 151720 Hom.: 7831 Cov.: 31

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.298 AC: 45257 AN: 151838 Hom.: 7833 Cov.: 31 AF XY: 0.293 AC XY: 21728 AN XY: 74220

African (AFR) AF: 0.488 AC: 20190 AN: 41332

American (AMR) AF: 0.210 AC: 3212 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1169 AN: 3470

East Asian (EAS) AF: 0.157 AC: 805 AN: 5132

South Asian (SAS) AF: 0.249 AC: 1195 AN: 4800

European-Finnish (FIN) AF: 0.216 AC: 2281 AN: 10572

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.229 AC: 15559 AN: 67940

Other (OTH) AF: 0.272 AC: 574 AN: 2108

Alfa AF: 0.258 Hom.: 4074

Bravo AF: 0.305

Asia WGS AF: 0.235 AC: 819 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.47
PhyloP100		-0.098

Splicing

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

Other links and lift over

dbSNP: rs1392705; hg19: chr3-193533201;