chr16-19393323-A-G

Variant names:

• chr16-19393323-A-G
• rs4780805
• ENST00000623838.1:n.146T>C

Variant summary

Our verdict is Benign. The variant received -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: ENSG00000280265 ENST00000623838.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.875
• Publications: 8 publications found

Genes affected

ENSG00000280265 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105371114	NR_188657.1	n.357+53T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000280265	ENST00000623838.1	n.146T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000259925	ENST00000563613.1	n.693+53T>C		intron_variant	Intron 3 of 4	5
ENSG00000259925	ENST00000717654.1	n.502+53T>C		intron_variant	Intron 1 of 2
ENSG00000259925	ENST00000717655.1	n.502+53T>C		intron_variant	Intron 1 of 4

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.971 AC: 40381 AN: 41594

American (AMR) AF: 0.811 AC: 12393 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.815 AC: 2827 AN: 3470

East Asian (EAS) AF: 0.692 AC: 3584 AN: 5176

South Asian (SAS) AF: 0.930 AC: 4490 AN: 4828

European-Finnish (FIN) AF: 0.752 AC: 7951 AN: 10576

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.851 AC: 57881 AN: 68024

Other (OTH) AF: 0.842 AC: 1781 AN: 2114

Alfa AF: 0.852 Hom.: 38323

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
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs4780805; hg19: chr16-19404645;