6-52198303-C-T

Variant names:

• chr6-52198303-C-T
• rs2154225

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 0.606 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.249 AC: 10320 AN: 41466

American (AMR) AF: 0.730 AC: 11153 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.621 AC: 2152 AN: 3466

East Asian (EAS) AF: 0.690 AC: 3565 AN: 5166

South Asian (SAS) AF: 0.646 AC: 3116 AN: 4822

European-Finnish (FIN) AF: 0.773 AC: 8167 AN: 10570

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.757 AC: 51464 AN: 67978

Other (OTH) AF: 0.636 AC: 1343 AN: 2110

Alfa AF: 0.698 Hom.: 47521

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
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs2154225; hg19: chr6-52063101;