rs8106822

chr19-31373516-G-A

Variant summary

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

The ENST00000585336.1(TSHZ3-AS1):n.251+12935G>A variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.424

Genes affected

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

LOC124904794 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TSHZ3-AS1	XR_002958388.2	n.27087+24599G>A		intron_variant, non_coding_transcript_variant
LOC124904794	XR_007067377.1	n.3361+5875G>A		intron_variant, non_coding_transcript_variant
TSHZ3-AS1	XR_001753896.2	n.209+21890G>A		intron_variant, non_coding_transcript_variant
TSHZ3-AS1	XR_001753900.2	n.209+21890G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSHZ3-AS1	ENST00000585336.1	n.251+12935G>A		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.437

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.606

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.502

Gnomad4 NFE AF: 0.396

Gnomad4 OTH AF: 0.382

Alfa AF: 0.418 Hom.: 1698

Bravo AF: 0.412

Asia WGS AF: 0.488 AC: 1695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.61
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8106822; hg19: chr19-31864422;