rs574933

chr6-25890903-C-Gchr6-25890903-C-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 0.399 in 151,978 control chromosomes in the GnomAD database, including 12,932 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 0.40 (12932 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200

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 (AFR) allele frequency at 95% confidence interval = 0.521 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: 0.399 AC: 60597 AN: 151860 Hom.: 12908 Cov.: 32

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.399 AC: 60667 AN: 151978 Hom.: 12932 Cov.: 32 AF XY: 0.398 AC XY: 29568 AN XY: 74314

Gnomad4 AFR AF: 0.526

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.280

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.506

Gnomad4 NFE AF: 0.358

Gnomad4 OTH AF: 0.364

Alfa AF: 0.379 Hom.: 1366

Bravo AF: 0.392

Asia WGS AF: 0.251 AC: 876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.1
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs574933; hg19: chr6-25891131;