rs11880316

Variant names:

• chr19-31420223-C-A
• rs11880316
• ENST00000786465.1:n.854C>A

Variant summary

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

The ENST00000716205.1(TSHZ3-AS1):​n.625-8C>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,242 control chromosomes in the GnomAD database, including 2,793 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 0.12 (2793 hom., cov: 33)
• Consequence: TSHZ3-AS1 ENST00000716205.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194
• Publications: 6 publications found

Genes affected

TSHZ3-AS1 (HGNC:55288): (TSHZ3 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000716205.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSHZ3-AS1	ENST00000786465.1		n.854C>A		non_coding_transcript_exon	Exon 1 of 2
	TSHZ3-AS1	ENST00000786466.1		n.127C>A		non_coding_transcript_exon	Exon 3 of 4
	TSHZ3-AS1	ENST00000786467.1		n.1332C>A		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17617 AN: 152124 Hom.: 2783 Cov.: 33

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0487

Gnomad ASJ AF: 0.0634

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.0211

Gnomad FIN AF: 0.0348

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0155

Gnomad OTH AF: 0.0844

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

GnomAD4 genome AF: 0.116 AC: 17676 AN: 152242 Hom.: 2793 Cov.: 33 AF XY: 0.114 AC XY: 8503 AN XY: 74440

African (AFR) AF: 0.361 AC: 14968 AN: 41500

American (AMR) AF: 0.0486 AC: 743 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0634 AC: 220 AN: 3470

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5184

South Asian (SAS) AF: 0.0209 AC: 101 AN: 4822

European-Finnish (FIN) AF: 0.0348 AC: 370 AN: 10620

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0155 AC: 1052 AN: 68040

Other (OTH) AF: 0.0835 AC: 176 AN: 2108

Alfa AF: 0.0492 Hom.: 2775

Bravo AF: 0.128

Asia WGS AF: 0.0360 AC: 127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	1.0
DANN	Benign	0.50
PhyloP100		-0.19

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11880316;

hg19: chr19-31911129;