6-50637569-C-G

Variant names:

• chr6-50637569-C-G
• rs280310

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 0.208 in 151,890 control chromosomes in the GnomAD database, including 5,102 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 0.21 (5102 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.478

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.454 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: 0.208 AC: 31588 AN: 151772 Hom.: 5080 Cov.: 32

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.00755

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0993

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.208 AC: 31649 AN: 151890 Hom.: 5102 Cov.: 32 AF XY: 0.204 AC XY: 15144 AN XY: 74230

Gnomad4 AFR AF: 0.459

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.00757

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.0993

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.184

Alfa AF: 0.0628 Hom.: 63

Bravo AF: 0.221

Asia WGS AF: 0.0870 AC: 303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.1
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs280310; hg19: chr6-50605282;