19-39245644-CATATATATATATATATAT-CATATATATATATATATATATATAT

Position:

• chr19-39245644-CATATATATATATATATAT-CATATATATATATATATATATATAT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.016 (25 hom., cov: 0)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0164 (2253/137584) while in subpopulation NFE AF= 0.0204 (1308/64272). AF 95% confidence interval is 0.0194. There are 25 homozygotes in gnomad4. There are 1051 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 25 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.39245644_39245645insATATAT		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0164 AC: 2252 AN: 137532 Hom.: 25 Cov.: 0

Gnomad AFR AF: 0.0126

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0103

Gnomad ASJ AF: 0.0233

Gnomad EAS AF: 0.00219

Gnomad SAS AF: 0.0184

Gnomad FIN AF: 0.0174

Gnomad MID AF: 0.0135

Gnomad NFE AF: 0.0203

Gnomad OTH AF: 0.0121

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

GnomAD4 genome AF: 0.0164 AC: 2253 AN: 137584 Hom.: 25 Cov.: 0 AF XY: 0.0159 AC XY: 1051 AN XY: 66014

Gnomad4 AFR AF: 0.0126

Gnomad4 AMR AF: 0.0103

Gnomad4 ASJ AF: 0.0233

Gnomad4 EAS AF: 0.00219

Gnomad4 SAS AF: 0.0187

Gnomad4 FIN AF: 0.0174

Gnomad4 NFE AF: 0.0204

Gnomad4 OTH AF: 0.0121

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: rs67461793; hg19: chr19-39736284;