chr19-31420223-C-A

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 ENST00000786465.1(TSHZ3-AS1):​n.854C>A 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 0.116 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 ENST00000786465.1 non_coding_transcript_exon
• 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSHZ3-AS1	XR_001753896.2	n.2947C>A		non_coding_transcript_exon_variant	Exon 3 of 3
TSHZ3-AS1	XR_001753900.2	n.2437C>A		non_coding_transcript_exon_variant	Exon 3 of 3
TSHZ3-AS1	XR_002958388.2	n.29825C>A		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSHZ3-AS1	ENST00000786465.1	n.854C>A		non_coding_transcript_exon_variant	Exon 1 of 2
TSHZ3-AS1	ENST00000786466.1	n.127C>A		non_coding_transcript_exon_variant	Exon 3 of 4
TSHZ3-AS1	ENST00000786467.1	n.1332C>A		non_coding_transcript_exon_variant	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 v4.3

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

Other links and lift over

dbSNP: rs11880316; hg19: chr19-31911129;