1-104087983-T-C

Variant names:

• chr1-104087983-T-C
• rs10494006
• ENST00000634580.1:n.922+14079T>C

Variant summary

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

The ENST00000634997.1(THAP3P1):​n.55-4025T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 151,820 control chromosomes in the GnomAD database, including 8,612 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 0.30 (8612 hom., cov: 32)
• Consequence: THAP3P1 ENST00000634997.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000634997.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	THAP3P1	ENST00000634580.1	TSL:5	n.922+14079T>C		intron	N/A
	THAP3P1	ENST00000634888.1	TSL:5	n.735+14079T>C		intron	N/A
	THAP3P1	ENST00000634997.1	TSL:4	n.55-4025T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45407 AN: 151702 Hom.: 8586 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.300 AC: 45476 AN: 151820 Hom.: 8612 Cov.: 32 AF XY: 0.305 AC XY: 22617 AN XY: 74216

African (AFR) AF: 0.482 AC: 19943 AN: 41390

American (AMR) AF: 0.407 AC: 6196 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 508 AN: 3466

East Asian (EAS) AF: 0.551 AC: 2829 AN: 5132

South Asian (SAS) AF: 0.274 AC: 1320 AN: 4816

European-Finnish (FIN) AF: 0.231 AC: 2436 AN: 10568

Middle Eastern (MID) AF: 0.134 AC: 39 AN: 292

European-Non Finnish (NFE) AF: 0.170 AC: 11569 AN: 67902

Other (OTH) AF: 0.267 AC: 561 AN: 2104

Alfa AF: 0.250 Hom.: 757

Bravo AF: 0.324

Asia WGS AF: 0.397 AC: 1379 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.26
DANN	Benign	0.55
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs10494006; hg19: chr1-104630605;