rs3214574

Variant names:

• chr19-41854712-CCT-C
• rs3214574

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The variant allele was found at a frequency of 0.157 in 152,238 control chromosomes in the GnomAD database, including 2,139 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.16 (2139 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.241 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: 0.157 AC: 23919 AN: 152120 Hom.: 2140 Cov.: 29

Gnomad AFR AF: 0.0655

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.157 AC: 23919 AN: 152238 Hom.: 2139 Cov.: 29 AF XY: 0.159 AC XY: 11865 AN XY: 74426

Gnomad4 AFR AF: 0.0654

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.252

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.240

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.170

Alfa AF: 0.176 Hom.: 314

Bravo AF: 0.147

Asia WGS AF: 0.195 AC: 678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3214574; hg19: chr19-42358780;