chr6-52198303-C-T

Variant names:

• chr6-52198303-C-T
• rs2154225

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 0.606 in 152,068 control chromosomes in the GnomAD database, including 31,783 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 0.61 (31783 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.291

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.752 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: 0.607 AC: 92166 AN: 151950 Hom.: 31776 Cov.: 33

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.773

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.757

Gnomad OTH AF: 0.634

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

GnomAD4 genome AF: 0.606 AC: 92186 AN: 152068 Hom.: 31783 Cov.: 33 AF XY: 0.609 AC XY: 45276 AN XY: 74328

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.730

Gnomad4 ASJ AF: 0.621

Gnomad4 EAS AF: 0.690

Gnomad4 SAS AF: 0.646

Gnomad4 FIN AF: 0.773

Gnomad4 NFE AF: 0.757

Gnomad4 OTH AF: 0.636

Alfa AF: 0.715 Hom.: 38148

Bravo AF: 0.588

Asia WGS AF: 0.649 AC: 2260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.1
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2154225; hg19: chr6-52063101;