19-44823407-C-T

Variant names:

• chr19-44823407-C-T
• rs10405693

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.285 in 151,964 control chromosomes in the GnomAD database, including 6,661 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.28 (6661 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.371
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.358 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: 0.285 AC: 43274 AN: 151846 Hom.: 6662 Cov.: 31

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.285 AC: 43290 AN: 151964 Hom.: 6661 Cov.: 31 AF XY: 0.289 AC XY: 21447 AN XY: 74248

African (AFR) AF: 0.179 AC: 7441 AN: 41454

American (AMR) AF: 0.366 AC: 5576 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1202 AN: 3472

East Asian (EAS) AF: 0.163 AC: 840 AN: 5164

South Asian (SAS) AF: 0.220 AC: 1058 AN: 4820

European-Finnish (FIN) AF: 0.386 AC: 4068 AN: 10546

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 22044 AN: 67956

Other (OTH) AF: 0.287 AC: 607 AN: 2114

Alfa AF: 0.300 Hom.: 3295

Bravo AF: 0.286

Asia WGS AF: 0.197 AC: 688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.9
DANN	Benign	0.70
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs10405693; hg19: chr19-45326664; COSMIC: COSV54305222;