rs1439010

Positions:

• chr3-152828806-A-G

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 0.31 in 152,168 control chromosomes in the GnomAD database, including 11,357 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 0.31 (11357 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.251

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47067 AN: 152050 Hom.: 11318 Cov.: 32

Gnomad AFR AF: 0.676

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.310 AC: 47161 AN: 152168 Hom.: 11357 Cov.: 32 AF XY: 0.307 AC XY: 22871 AN XY: 74414

Gnomad4 AFR AF: 0.676

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.283

Alfa AF: 0.235 Hom.: 918

Bravo AF: 0.337

Asia WGS AF: 0.272 AC: 949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1439010; hg19: chr3-152546595;