16-19393323-A-G

Position:

• chr16-19393323-A-G

Variant summary

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

The ENST00000623838.1(ENSG00000280265):​n.146T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.869 in 152,274 control chromosomes in the GnomAD database, including 58,005 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 0.87 (58005 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: ENST00000623838.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.875

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.963 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105371114	XR_001752097.2	n.357+53T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000623838.1	n.146T>C		non_coding_transcript_exon_variant	1/1
	ENST00000563613.1	n.693+53T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.869 AC: 132285 AN: 152156 Hom.: 57946 Cov.: 33

Gnomad AFR AF: 0.971

Gnomad AMI AF: 0.947

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.815

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.930

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.851

Gnomad OTH AF: 0.841

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.869 AC: 132396 AN: 152274 Hom.: 58005 Cov.: 33 AF XY: 0.863 AC XY: 64239 AN XY: 74428

Gnomad4 AFR AF: 0.971

Gnomad4 AMR AF: 0.811

Gnomad4 ASJ AF: 0.815

Gnomad4 EAS AF: 0.692

Gnomad4 SAS AF: 0.930

Gnomad4 FIN AF: 0.752

Gnomad4 NFE AF: 0.851

Gnomad4 OTH AF: 0.842

Alfa AF: 0.850 Hom.: 31157

Bravo AF: 0.875

Asia WGS AF: 0.846 AC: 2943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4780805; hg19: chr16-19404645;