rs574933

Variant names:

• chr6-25890903-C-G
• rs574933

Your query was ambiguous. Multiple possible variants found:

• chr6-25890903-C-G
• chr6-25890903-C-T

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 0.399 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.526 AC: 21811 AN: 41434

American (AMR) AF: 0.307 AC: 4693 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 970 AN: 3466

East Asian (EAS) AF: 0.262 AC: 1352 AN: 5164

South Asian (SAS) AF: 0.211 AC: 1021 AN: 4828

European-Finnish (FIN) AF: 0.506 AC: 5338 AN: 10552

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.358 AC: 24286 AN: 67922

Other (OTH) AF: 0.364 AC: 769 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.1
DANN	Benign	0.75
PhyloP100		-0.0020

Splicing

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

Other links and lift over

dbSNP: rs574933; hg19: chr6-25891131;