rs373552

chr6-52937230-A-Gchr6-52937230-A-T

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 0.182 in 152,122 control chromosomes in the GnomAD database, including 3,302 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 0.18 (3302 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.353

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27663 AN: 152004 Hom.: 3298 Cov.: 31

Gnomad AFR AF: 0.0532

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.0417

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.182 AC: 27656 AN: 152122 Hom.: 3302 Cov.: 31 AF XY: 0.178 AC XY: 13268 AN XY: 74354

Gnomad4 AFR AF: 0.0531

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.287

Gnomad4 EAS AF: 0.0408

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.260

Gnomad4 OTH AF: 0.209

Alfa AF: 0.242 Hom.: 6534

Bravo AF: 0.175

Asia WGS AF: 0.0740 AC: 259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	6.1
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs373552; hg19: chr6-52802028;