rs6449586

Variant names:

• chr5-51339044-C-T
• rs6449586

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.626 in 152,086 control chromosomes in the GnomAD database, including 31,749 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 0.63 (31749 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.842 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: 0.626 AC: 95110 AN: 151968 Hom.: 31692 Cov.: 32

Gnomad AFR AF: 0.849

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.626 AC: 95237 AN: 152086 Hom.: 31749 Cov.: 32 AF XY: 0.621 AC XY: 46191 AN XY: 74328

African (AFR) AF: 0.849 AC: 35259 AN: 41526

American (AMR) AF: 0.493 AC: 7539 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1752 AN: 3466

East Asian (EAS) AF: 0.226 AC: 1168 AN: 5166

South Asian (SAS) AF: 0.476 AC: 2296 AN: 4824

European-Finnish (FIN) AF: 0.652 AC: 6874 AN: 10538

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.566 AC: 38473 AN: 67968

Other (OTH) AF: 0.583 AC: 1230 AN: 2110

Alfa AF: 0.580 Hom.: 75690

Bravo AF: 0.621

Asia WGS AF: 0.421 AC: 1463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.12
DANN	Benign	0.50
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs6449586; hg19: chr5-50634878;