rs10748180

Variant names:

• chr12-71677265-A-C
• rs10748180
• NM_031435.4:c.*157A>C

Your query was ambiguous. Multiple possible variants found:

• chr12-71677265-A-C
• chr12-71677265-A-G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_031435.4(THAP2):​c.*157A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000744 in 660,184 control chromosomes in the GnomAD database, including 1 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 0.00083 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00072 (1 hom.)
• Consequence: THAP2 NM_031435.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69
• Publications: 8 publications found

Genes affected

THAP2 (HGNC:20854): (THAP domain containing 2) Predicted to enable DNA binding activity and metal ion binding activity. Located in nucleolus. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000258064 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
THAP2	NM_031435.4	c.*157A>C		3_prime_UTR_variant	Exon 3 of 3	ENST00000308086.3	NP_113623.1
LOC124902965	XR_007063367.1	n.144-5483T>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
THAP2	ENST00000308086.3	c.*157A>C		3_prime_UTR_variant	Exon 3 of 3	1	NM_031435.4	ENSP00000310796.2
ENSG00000258064	ENST00000548802.1	n.195+2867A>C		intron_variant	Intron 1 of 4	3		ENSP00000454911.2
ENSG00000306515	ENST00000819198.1	n.154-5483T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.000835 AC: 127 AN: 152042 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.0000242

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000327

Gnomad ASJ AF: 0.0233

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000530

Gnomad OTH AF: 0.00191

GnomAD4 exome AF: 0.000717 AC: 364 AN: 508024 Hom.: 1 Cov.: 7 AF XY: 0.000796 AC XY: 200 AN XY: 251234

African (AFR) AF: 0.0000874 AC: 1 AN: 11448

American (AMR) AF: 0.000918 AC: 9 AN: 9808

Ashkenazi Jewish (ASJ) AF: 0.0178 AC: 195 AN: 10966

East Asian (EAS) AF: 0.0000410 AC: 1 AN: 24372

South Asian (SAS) AF: 0.0000780 AC: 1 AN: 12814

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 21588

Middle Eastern (MID) AF: 0.00450 AC: 8 AN: 1776

European-Non Finnish (NFE) AF: 0.000236 AC: 92 AN: 390240

Other (OTH) AF: 0.00228 AC: 57 AN: 25012

GnomAD4 genome AF: 0.000835 AC: 127 AN: 152160 Hom.: 0 Cov.: 33 AF XY: 0.000780 AC XY: 58 AN XY: 74390

African (AFR) AF: 0.0000241 AC: 1 AN: 41526

American (AMR) AF: 0.000327 AC: 5 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0233 AC: 81 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5190

South Asian (SAS) AF: 0.00 AC: 0 AN: 4822

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10580

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000530 AC: 36 AN: 67964

Other (OTH) AF: 0.00189 AC: 4 AN: 2112

Alfa AF: 0.00 Hom.: 23604

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.084
DANN	Benign	0.26
PhyloP100		-1.7
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: rs10748180; hg19: chr12-72071045;