19-39245644-CATATATATATATATATAT-CATATATATATATATATATATAT

Variant names:

• chr19-39245644-C-CATAT
• 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 0.032 (91 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 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 the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 91 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: 0.0323 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

African (AFR) AF: 0.0295 AC: 1096 AN: 37210

American (AMR) AF: 0.0314 AC: 419 AN: 13332

Ashkenazi Jewish (ASJ) AF: 0.0673 AC: 225 AN: 3342

East Asian (EAS) AF: 0.00482 AC: 22 AN: 4562

South Asian (SAS) AF: 0.0421 AC: 173 AN: 4114

European-Finnish (FIN) AF: 0.0171 AC: 131 AN: 7652

Middle Eastern (MID) AF: 0.0410 AC: 11 AN: 268

European-Non Finnish (NFE) AF: 0.0338 AC: 2171 AN: 64244

Other (OTH) AF: 0.0488 AC: 93 AN: 1906

Alfa AF: 0.0140 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;