19-39245644-CATATATATATATATATAT-CATATATATATATATATATATAT

Position:

• chr19-39245644-CATATATATATATATATAT-CATATATATATATATATATATAT

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 0.032 (91 hom., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0323 (4441/137488) while in subpopulation SAS AF= 0.0421 (173/4114). AF 95% confidence interval is 0.0369. There are 91 homozygotes in gnomad4. There are 2040 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 91 gene

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0323 AC: 4442 AN: 137436 Hom.: 91 Cov.: 0

Gnomad AFR AF: 0.0295

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.0315

Gnomad ASJ AF: 0.0673

Gnomad EAS AF: 0.00481

Gnomad SAS AF: 0.0421

Gnomad FIN AF: 0.0171

Gnomad MID AF: 0.0374

Gnomad NFE AF: 0.0338

Gnomad OTH AF: 0.0491

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

GnomAD4 genome AF: 0.0323 AC: 4441 AN: 137488 Hom.: 91 Cov.: 0 AF XY: 0.0309 AC XY: 2040 AN XY: 65974

Gnomad4 AFR AF: 0.0295

Gnomad4 AMR AF: 0.0314

Gnomad4 ASJ AF: 0.0673

Gnomad4 EAS AF: 0.00482

Gnomad4 SAS AF: 0.0421

Gnomad4 FIN AF: 0.0171

Gnomad4 NFE AF: 0.0338

Gnomad4 OTH AF: 0.0488

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;