rs16973285

chr19-39254056-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0755 in 143,062 control chromosomes in the GnomAD database, including 459 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 0.076 (459 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0911 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0756 AC: 10802 AN: 142978 Hom.: 459 Cov.: 25

Gnomad AFR AF: 0.0531

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.0632

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.00546

Gnomad SAS AF: 0.0469

Gnomad FIN AF: 0.0790

Gnomad MID AF: 0.0764

Gnomad NFE AF: 0.0931

Gnomad OTH AF: 0.0739

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

GnomAD4 genome AF: 0.0755 AC: 10806 AN: 143062 Hom.: 459 Cov.: 25 AF XY: 0.0740 AC XY: 5092 AN XY: 68786

Gnomad4 AFR AF: 0.0531

Gnomad4 AMR AF: 0.0630

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.00548

Gnomad4 SAS AF: 0.0473

Gnomad4 FIN AF: 0.0790

Gnomad4 NFE AF: 0.0931

Gnomad4 OTH AF: 0.0730

Alfa AF: 0.0910 Hom.: 874

Bravo AF: 0.0746

Asia WGS AF: 0.0310 AC: 107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.4
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16973285; hg19: chr19-39744696;