19-39245644-CATATATATATATATATAT-CATATATATATATATATATATATAT

Variant names:

• chr19-39245644-C-CATATAT
• rs67461793

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 25 gene

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: 0.0164 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

African (AFR) AF: 0.0126 AC: 468 AN: 37254

American (AMR) AF: 0.0103 AC: 137 AN: 13346

Ashkenazi Jewish (ASJ) AF: 0.0233 AC: 78 AN: 3346

East Asian (EAS) AF: 0.00219 AC: 10 AN: 4560

South Asian (SAS) AF: 0.0187 AC: 77 AN: 4110

European-Finnish (FIN) AF: 0.0174 AC: 133 AN: 7658

Middle Eastern (MID) AF: 0.0111 AC: 3 AN: 270

European-Non Finnish (NFE) AF: 0.0204 AC: 1308 AN: 64272

Other (OTH) AF: 0.0121 AC: 23 AN: 1908

Alfa AF: 0.00 Hom.: 677

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs67461793; hg19: chr19-39736284;