chr3-21299371-T-C

Position:

• chr3-21299371-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 0.4 in 151,882 control chromosomes in the GnomAD database, including 13,197 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 0.40 (13197 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.5 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: 0.400 AC: 60772 AN: 151764 Hom.: 13192 Cov.: 31

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.400 AC: 60802 AN: 151882 Hom.: 13197 Cov.: 31 AF XY: 0.395 AC XY: 29356 AN XY: 74240

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.319

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.468

Gnomad4 NFE AF: 0.504

Gnomad4 OTH AF: 0.416

Alfa AF: 0.426 Hom.: 2023

Bravo AF: 0.383

Asia WGS AF: 0.201 AC: 699 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.7
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs617991; hg19: chr3-21340863;