rs9834970

chr3-36814539-T-C

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 0.45 in 152,054 control chromosomes in the GnomAD database, including 16,143 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 0.45 (16143 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.712

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68455 AN: 151936 Hom.: 16130 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.450 AC: 68497 AN: 152054 Hom.: 16143 Cov.: 32 AF XY: 0.450 AC XY: 33430 AN XY: 74330

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.558

Gnomad4 ASJ AF: 0.487

Gnomad4 EAS AF: 0.605

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.392

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.468

Alfa AF: 0.498 Hom.: 22278

Bravo AF: 0.455

Asia WGS AF: 0.546 AC: 1897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
Cadd	Benign	3.2
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9834970; hg19: chr3-36856030;