rs12414547

Variant names:

• chr10-5696885-T-C
• rs12414547
• NM_001321783.2:c.-361+11710T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TASOR2	NM_001321783.2	c.-361+11710T>C		intron_variant	Intron 1 of 21	ENST00000695737.1	NP_001308712.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TASOR2	ENST00000695737.1	c.-361+11710T>C		intron_variant	Intron 1 of 21		NM_001321783.2	ENSP00000512130.1

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

African (AFR) AF: 0.00532 AC: 221 AN: 41538

American (AMR) AF: 0.0598 AC: 915 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0421 AC: 146 AN: 3470

East Asian (EAS) AF: 0.000385 AC: 2 AN: 5194

South Asian (SAS) AF: 0.0158 AC: 76 AN: 4822

European-Finnish (FIN) AF: 0.0119 AC: 126 AN: 10560

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0202 AC: 1373 AN: 68020

Other (OTH) AF: 0.0161 AC: 34 AN: 2110

Alfa AF: 0.0189 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
PhyloP100		0.14
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs12414547; hg19: chr10-5738848;