rs6446298

Variant names:

• chr3-49823421-T-C
• rs6446298

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 0.624 in 151,996 control chromosomes in the GnomAD database, including 30,630 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 0.62 (30630 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.705 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: 0.624 AC: 94772 AN: 151878 Hom.: 30600 Cov.: 32

Gnomad AFR AF: 0.712

Gnomad AMI AF: 0.752

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.621

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.624 AC: 94845 AN: 151996 Hom.: 30630 Cov.: 32 AF XY: 0.611 AC XY: 45389 AN XY: 74264

Gnomad4 AFR AF: 0.712

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.631

Gnomad4 EAS AF: 0.217

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.538

Gnomad4 NFE AF: 0.653

Gnomad4 OTH AF: 0.642

Alfa AF: 0.643 Hom.: 63764

Bravo AF: 0.626

Asia WGS AF: 0.455 AC: 1585 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6446298; hg19: chr3-49860854;