3-12260963-C-T

Variant names:

• chr3-12260963-C-T
• rs9878908

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 0.829 in 152,176 control chromosomes in the GnomAD database, including 52,545 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 0.83 (52545 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.888 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: 0.829 AC: 125991 AN: 152058 Hom.: 52481 Cov.: 31

Gnomad AFR AF: 0.896

Gnomad AMI AF: 0.892

Gnomad AMR AF: 0.841

Gnomad ASJ AF: 0.873

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.844

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.858

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

GnomAD4 genome AF: 0.829 AC: 126112 AN: 152176 Hom.: 52545 Cov.: 31 AF XY: 0.830 AC XY: 61747 AN XY: 74406

Gnomad4 AFR AF: 0.896

Gnomad4 AMR AF: 0.842

Gnomad4 ASJ AF: 0.873

Gnomad4 EAS AF: 0.598

Gnomad4 SAS AF: 0.844

Gnomad4 FIN AF: 0.821

Gnomad4 NFE AF: 0.798

Gnomad4 OTH AF: 0.860

Alfa AF: 0.808 Hom.: 80770

Bravo AF: 0.832

Asia WGS AF: 0.796 AC: 2769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.9
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9878908; hg19: chr3-12302462;