rs9831754

Positions:

• chr3-78304441-T-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 0.199 in 152,018 control chromosomes in the GnomAD database, including 3,687 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 0.20 (3687 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.424 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: 0.199 AC: 30209 AN: 151904 Hom.: 3672 Cov.: 32

Gnomad AFR AF: 0.0931

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.199 AC: 30235 AN: 152018 Hom.: 3687 Cov.: 32 AF XY: 0.204 AC XY: 15193 AN XY: 74308

Gnomad4 AFR AF: 0.0929

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.439

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.287

Gnomad4 NFE AF: 0.213

Gnomad4 OTH AF: 0.166

Alfa AF: 0.219 Hom.: 4443

Bravo AF: 0.195

Asia WGS AF: 0.326 AC: 1129 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	10
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9831754; hg19: chr3-78353591;