rs1928313

Variant names:

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

Variant summary

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

The ENST00000634997.1(ENSG00000215869):​n.252-14103C>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: ENSG00000215869 ENST00000634997.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409

Genes affected

ENSG00000215869 (HGNC:56895): (THAP3 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000215869	ENST00000634580.1	n.923-14103C>T		intron_variant	Intron 1 of 1	5
ENSG00000215869	ENST00000634888.1	n.735+37555C>T		intron_variant	Intron 1 of 3	5
ENSG00000215869	ENST00000634997.1	n.252-14103C>T		intron_variant	Intron 2 of 2	4

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

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.0251

Gnomad4 ASJ AF: 0.0268

Gnomad4 EAS AF: 0.0168

Gnomad4 SAS AF: 0.0344

Gnomad4 FIN AF: 0.00933

Gnomad4 NFE AF: 0.0134

Gnomad4 OTH AF: 0.0402

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1928313; hg19: chr1-104654081;