rs12414547

chr10-5696885-T-C

Variant summary

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

The NM_001321783.2(TASOR2):c.-361+11710T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.019 in 152,218 control chromosomes in the GnomAD database, including 42 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 0.019 (42 hom., cov: 33)
• Consequence: TASOR2 NM_001321783.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.139

Genes affected

TASOR2 (HGNC:23484): (transcription activation suppressor family member 2) Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0566 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TASOR2	NM_001321783.2	c.-361+11710T>C		intron_variant		ENST00000695737.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TASOR2	ENST00000695737.1	c.-361+11710T>C		intron_variant			NM_001321783.2

Frequencies

GnomAD3 genomes AF: 0.0190 AC: 2893 AN: 152100 Hom.: 43 Cov.: 33

Gnomad AFR AF: 0.00534

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0597

Gnomad ASJ AF: 0.0421

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0157

Gnomad FIN AF: 0.0119

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0202

Gnomad OTH AF: 0.0163

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

GnomAD4 genome AF: 0.0190 AC: 2895 AN: 152218 Hom.: 42 Cov.: 33 AF XY: 0.0193 AC XY: 1435 AN XY: 74434

Gnomad4 AFR AF: 0.00532

Gnomad4 AMR AF: 0.0598

Gnomad4 ASJ AF: 0.0421

Gnomad4 EAS AF: 0.000385

Gnomad4 SAS AF: 0.0158

Gnomad4 FIN AF: 0.0119

Gnomad4 NFE AF: 0.0202

Gnomad4 OTH AF: 0.0161

Alfa AF: 0.0191 Hom.: 5

Bravo AF: 0.0230

Asia WGS AF: 0.0120 AC: 45 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.9
Dann	Benign	0.43

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs12414547; hg19: chr10-5738848;