rs6763848

chr3-1470903-C-Achr3-1470903-C-Gchr3-1470903-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;