3-1470903-C-A

Variant names:

• chr3-1470903-C-A
• rs6763848

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 152,088 control chromosomes in the GnomAD database, including 7,919 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 (7919 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.65 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: 0.310 AC: 47175 AN: 151970 Hom.: 7919 Cov.: 33

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.668

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.310 AC: 47189 AN: 152088 Hom.: 7919 Cov.: 33 AF XY: 0.315 AC XY: 23449 AN XY: 74324

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.668

Gnomad4 SAS AF: 0.524

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.318

Alfa AF: 0.299 Hom.: 7207

Bravo AF: 0.306

Asia WGS AF: 0.575 AC: 1998 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6763848; hg19: chr3-1512587;