chr1-104111459-C-T

Variant names:

• chr1-104111459-C-T
• rs1928313
• ENST00000634580.1:n.923-14103C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000634580.1(THAP3P1):​n.923-14103C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0434 in 152,210 control chromosomes in the GnomAD database, including 303 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 0.043 (303 hom., cov: 32)
• Consequence: THAP3P1 ENST00000634580.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409
• Publications: 3 publications found

Genes affected

THAP3P1 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000634580.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	THAP3P1	ENST00000634580.1	TSL:5	n.923-14103C>T		intron	N/A
	THAP3P1	ENST00000634888.1	TSL:5	n.735+37555C>T		intron	N/A
	THAP3P1	ENST00000634997.1	TSL:4	n.252-14103C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0432 AC: 6577 AN: 152092 Hom.: 301 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0252

Gnomad ASJ AF: 0.0268

Gnomad EAS AF: 0.0168

Gnomad SAS AF: 0.0339

Gnomad FIN AF: 0.00933

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0134

Gnomad OTH AF: 0.0407

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

GnomAD4 genome AF: 0.0434 AC: 6605 AN: 152210 Hom.: 303 Cov.: 32 AF XY: 0.0439 AC XY: 3268 AN XY: 74422

African (AFR) AF: 0.114 AC: 4748 AN: 41528

American (AMR) AF: 0.0251 AC: 383 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0268 AC: 93 AN: 3472

East Asian (EAS) AF: 0.0168 AC: 87 AN: 5170

South Asian (SAS) AF: 0.0344 AC: 166 AN: 4828

European-Finnish (FIN) AF: 0.00933 AC: 99 AN: 10614

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0134 AC: 909 AN: 68004

Other (OTH) AF: 0.0402 AC: 85 AN: 2112

Alfa AF: 0.0289 Hom.: 32

Bravo AF: 0.0481

Asia WGS AF: 0.0330 AC: 114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.77
DANN	Benign	0.23
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs1928313; hg19: chr1-104654081;