19-20668253-C-T

Variant names:

• chr19-20668253-C-T
• rs4402690
• ENST00000805334.1:n.71+5222C>T

Variant summary

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

The ENST00000805334.1(ENSG00000304675):​n.71+5222C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 150,878 control chromosomes in the GnomAD database, including 7,102 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 0.30 (7102 hom., cov: 29)
• Consequence: ENSG00000304675 ENST00000805334.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.812
• Publications: 4 publications found

Genes affected

ENSG00000304675 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.356 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
ENSG00000304675	ENST00000805334.1	n.71+5222C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45395 AN: 150764 Hom.: 7093 Cov.: 29

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.301 AC: 45442 AN: 150878 Hom.: 7102 Cov.: 29 AF XY: 0.300 AC XY: 22050 AN XY: 73598

African (AFR) AF: 0.361 AC: 14804 AN: 41060

American (AMR) AF: 0.349 AC: 5288 AN: 15150

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 785 AN: 3464

East Asian (EAS) AF: 0.353 AC: 1801 AN: 5096

South Asian (SAS) AF: 0.240 AC: 1143 AN: 4760

European-Finnish (FIN) AF: 0.222 AC: 2283 AN: 10288

Middle Eastern (MID) AF: 0.212 AC: 62 AN: 292

European-Non Finnish (NFE) AF: 0.273 AC: 18501 AN: 67758

Other (OTH) AF: 0.280 AC: 589 AN: 2100

Alfa AF: 0.142 Hom.: 246

Bravo AF: 0.314

Asia WGS AF: 0.316 AC: 1101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.70
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs4402690; hg19: chr19-20851059;