19-40989850-T-C

Variant names:

• chr19-40989850-T-C
• rs2054675

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 0.289 in 151,818 control chromosomes in the GnomAD database, including 6,908 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 0.29 (6908 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.829
• Publications: 21 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43875 AN: 151700 Hom.: 6905 Cov.: 31

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.289 AC: 43892 AN: 151818 Hom.: 6908 Cov.: 31 AF XY: 0.289 AC XY: 21415 AN XY: 74190

African (AFR) AF: 0.385 AC: 15890 AN: 41314

American (AMR) AF: 0.343 AC: 5225 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 939 AN: 3470

East Asian (EAS) AF: 0.212 AC: 1094 AN: 5150

South Asian (SAS) AF: 0.383 AC: 1840 AN: 4798

European-Finnish (FIN) AF: 0.182 AC: 1922 AN: 10578

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16118 AN: 67956

Other (OTH) AF: 0.306 AC: 643 AN: 2104

Alfa AF: 0.250 Hom.: 8317

Bravo AF: 0.301

Asia WGS AF: 0.324 AC: 1122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.63
DANN	Benign	0.36
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs2054675; hg19: chr19-41495755;