chr19-31373516-G-A

Variant names:

• chr19-31373516-G-A
• rs8106822
• ENST00000585336.1:n.251+12935G>A

Variant summary

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

The ENST00000585336.1(TSHZ3-AS1):​n.251+12935G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 152,070 control chromosomes in the GnomAD database, including 13,629 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 0.42 (13629 hom., cov: 32)
• Consequence: TSHZ3-AS1 ENST00000585336.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.424
• Publications: 3 publications found

Genes affected

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

LOC124904794 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000585336.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSHZ3-AS1	ENST00000585336.1	TSL:4	n.251+12935G>A		intron	N/A
	TSHZ3-AS1	ENST00000716204.1		n.308+24599G>A		intron	N/A
	TSHZ3-AS1	ENST00000716205.1		n.220+24599G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63609 AN: 151952 Hom.: 13607 Cov.: 32

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.419 AC: 63672 AN: 152070 Hom.: 13629 Cov.: 32 AF XY: 0.424 AC XY: 31500 AN XY: 74326

African (AFR) AF: 0.437 AC: 18136 AN: 41468

American (AMR) AF: 0.418 AC: 6396 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 851 AN: 3470

East Asian (EAS) AF: 0.606 AC: 3126 AN: 5158

South Asian (SAS) AF: 0.400 AC: 1924 AN: 4812

European-Finnish (FIN) AF: 0.502 AC: 5314 AN: 10580

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.396 AC: 26891 AN: 67978

Other (OTH) AF: 0.382 AC: 806 AN: 2110

Alfa AF: 0.419 Hom.: 1767

Bravo AF: 0.412

Asia WGS AF: 0.488 AC: 1695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.61
DANN	Benign	0.38
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs8106822; hg19: chr19-31864422;