3-3189963-C-T

Variant names:

• chr3-3189963-C-T
• rs3856852

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 0.104 in 152,118 control chromosomes in the GnomAD database, including 901 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 0.10 (901 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.722

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 (NFE) allele frequency at 95% confidence interval = 0.132 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: 0.104 AC: 15746 AN: 152000 Hom.: 896 Cov.: 33

Gnomad AFR AF: 0.0755

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.0839

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.0203

Gnomad SAS AF: 0.0609

Gnomad FIN AF: 0.0871

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.104 AC: 15762 AN: 152118 Hom.: 901 Cov.: 33 AF XY: 0.0996 AC XY: 7404 AN XY: 74346

Gnomad4 AFR AF: 0.0757

Gnomad4 AMR AF: 0.0838

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.0203

Gnomad4 SAS AF: 0.0612

Gnomad4 FIN AF: 0.0871

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.0991

Alfa AF: 0.121 Hom.: 546

Bravo AF: 0.103

Asia WGS AF: 0.0450 AC: 156 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	4.9
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3856852; hg19: chr3-3231647;