19-21691444-C-T

Variant names:

• chr19-21691444-C-T
• rs12979680

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 0.153 in 152,118 control chromosomes in the GnomAD database, including 1,934 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 0.15 (1934 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.19 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: 0.153 AC: 23229 AN: 152000 Hom.: 1932 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.0183

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.153 AC: 23249 AN: 152118 Hom.: 1934 Cov.: 32 AF XY: 0.149 AC XY: 11097 AN XY: 74356

African (AFR) AF: 0.185 AC: 7664 AN: 41480

American (AMR) AF: 0.121 AC: 1845 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 700 AN: 3472

East Asian (EAS) AF: 0.0182 AC: 94 AN: 5174

South Asian (SAS) AF: 0.200 AC: 964 AN: 4814

European-Finnish (FIN) AF: 0.106 AC: 1119 AN: 10586

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.151 AC: 10270 AN: 67998

Other (OTH) AF: 0.169 AC: 356 AN: 2104

Alfa AF: 0.105 Hom.: 221

Bravo AF: 0.156

Asia WGS AF: 0.130 AC: 453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.20
DANN	Benign	0.69
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs12979680; hg19: chr19-21874246;