rs6449612

Variant names:

• chr5-51405268-C-T
• rs6449612

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 0.419 in 151,918 control chromosomes in the GnomAD database, including 14,101 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 0.42 (14101 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.760

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 (AFR) allele frequency at 95% confidence interval = 0.551 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: 0.419 AC: 63538 AN: 151800 Hom.: 14083 Cov.: 32

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.419 AC: 63596 AN: 151918 Hom.: 14101 Cov.: 32 AF XY: 0.411 AC XY: 30540 AN XY: 74250

Gnomad4 AFR AF: 0.557

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.287

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.379

Gnomad4 NFE AF: 0.386

Gnomad4 OTH AF: 0.394

Alfa AF: 0.392 Hom.: 5621

Bravo AF: 0.423

Asia WGS AF: 0.293 AC: 1020 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.31
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6449612; hg19: chr5-50701102;