19-39245644-CATATATATATATATATAT-CATATATATATATATATATAT

Variant names:

• chr19-39245644-C-CAT
• rs67461793

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

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

• Frequency: Genomes: 𝑓 0.14 (1308 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.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

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: 0.139 AC: 19074 AN: 137128 Hom.: 1306 Cov.: 0

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.0874

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.0302

Gnomad SAS AF: 0.0908

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.216

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.139 AC: 19072 AN: 137178 Hom.: 1308 Cov.: 0 AF XY: 0.139 AC XY: 9141 AN XY: 65812

African (AFR) AF: 0.159 AC: 5892 AN: 37096

American (AMR) AF: 0.121 AC: 1615 AN: 13300

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 482 AN: 3338

East Asian (EAS) AF: 0.0298 AC: 136 AN: 4560

South Asian (SAS) AF: 0.0900 AC: 370 AN: 4110

European-Finnish (FIN) AF: 0.152 AC: 1155 AN: 7592

Middle Eastern (MID) AF: 0.230 AC: 62 AN: 270

European-Non Finnish (NFE) AF: 0.140 AC: 9007 AN: 64156

Other (OTH) AF: 0.146 AC: 278 AN: 1898

Alfa AF: 0.115 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;