6-54536491-T-C

Variant names:

• chr6-54536491-T-C
• rs659446

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 0.232 in 151,832 control chromosomes in the GnomAD database, including 5,402 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 0.23 (5402 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0460

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 (EAS) allele frequency at 95% confidence interval = 0.533 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: 0.232 AC: 35144 AN: 151714 Hom.: 5393 Cov.: 31

Gnomad AFR AF: 0.0598

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.232 AC: 35154 AN: 151832 Hom.: 5402 Cov.: 31 AF XY: 0.240 AC XY: 17774 AN XY: 74176

Gnomad4 AFR AF: 0.0597

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.259

Gnomad4 EAS AF: 0.550

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.273

Alfa AF: 0.248 Hom.: 954

Bravo AF: 0.237

Asia WGS AF: 0.334 AC: 1162 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.8
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs659446; hg19: chr6-54401289;