6-56429484-C-T

Variant names:

• chr6-56429484-C-T
• rs657057

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 0.55 in 151,868 control chromosomes in the GnomAD database, including 24,782 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 0.55 (24782 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.336

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.711 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: 0.550 AC: 83490 AN: 151748 Hom.: 24766 Cov.: 31

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.550 AC: 83543 AN: 151868 Hom.: 24782 Cov.: 31 AF XY: 0.557 AC XY: 41379 AN XY: 74226

Gnomad4 AFR AF: 0.309

Gnomad4 AMR AF: 0.618

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.731

Gnomad4 SAS AF: 0.590

Gnomad4 FIN AF: 0.742

Gnomad4 NFE AF: 0.638

Gnomad4 OTH AF: 0.542

Alfa AF: 0.598 Hom.: 13165

Bravo AF: 0.530

Asia WGS AF: 0.641 AC: 2229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.4
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs657057; hg19: chr6-56294282;