chr19-41854712-CCT-C

Position:

• chr19-41854712-CCT-C

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.41854713_41854714delCT		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;