rs1353540

Positions:

• chr19-31207281-C-A
• chr19-31207281-C-G
• chr19-31207281-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_138035.2(TSHZ3):​n.393+20724G>T variant causes a intron change. The variant allele was found at a frequency of 0.718 in 152,128 control chromosomes in the GnomAD database, including 39,804 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 0.72 (39804 hom., cov: 33)
• Consequence: TSHZ3 NR_138035.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.89

Genes affected

LINC01791 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.84 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TSHZ3	NR_138035.2	n.393+20724G>T		intron_variant
TSHZ3	NR_138036.2	n.394-2203G>T		intron_variant
LINC01791	NR_147209.1	n.519-218C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01791	ENST00000589511.1	n.513-218C>A		intron_variant		5
TSHZ3	ENST00000651361.1	n.687-2203G>T		intron_variant
LINC01791	ENST00000654096.1	n.197-3876C>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109190 AN: 152010 Hom.: 39746 Cov.: 33

Gnomad AFR AF: 0.847

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.726

Gnomad ASJ AF: 0.742

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.718 AC: 109303 AN: 152128 Hom.: 39804 Cov.: 33 AF XY: 0.717 AC XY: 53313 AN XY: 74366

Gnomad4 AFR AF: 0.847

Gnomad4 AMR AF: 0.726

Gnomad4 ASJ AF: 0.742

Gnomad4 EAS AF: 0.589

Gnomad4 SAS AF: 0.688

Gnomad4 FIN AF: 0.629

Gnomad4 NFE AF: 0.665

Gnomad4 OTH AF: 0.686

Alfa AF: 0.708 Hom.: 6518

Bravo AF: 0.732

Asia WGS AF: 0.643 AC: 2232 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	20
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1353540; hg19: chr19-31698187;