1-24364647-T-C

Variant names:

• chr1-24364647-T-C
• rs12079868
• NM_001199013.2:c.738-3606A>G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001199013.2(STPG1):​c.738-3606A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,116 control chromosomes in the GnomAD database, including 2,418 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.12 (2418 hom., cov: 32)
• Consequence: STPG1 NM_001199013.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.419

Genes affected

STPG1 (HGNC:28070): (sperm tail PG-rich repeat containing 1) Involved in positive regulation of apoptotic process and positive regulation of mitochondrial membrane permeability involved in apoptotic process. Predicted to be located in mitochondrion and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

GRHL3 (HGNC:25839): (grainyhead like transcription factor 3) This gene encodes a member of the grainyhead family of transcription factors. The encoded protein may function as a transcription factor during development, and has been shown to stimulate migration of endothelial cells. Multiple transcript variants encoding distinct isoforms have been identified for this gene.[provided by RefSeq, Aug 2010]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 1-24364647-T-C is Benign according to our data. Variant chr1-24364647-T-C is described in ClinVar as [Benign]. Clinvar id is 1272581.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STPG1	NM_001199013.2	c.738-3606A>G		intron_variant	Intron 7 of 8	ENST00000337248.9	NP_001185942.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STPG1	ENST00000337248.9	c.738-3606A>G		intron_variant	Intron 7 of 8	5	NM_001199013.2	ENSP00000337461.4

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18377 AN: 151998 Hom.: 2408 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0898

Gnomad ASJ AF: 0.0395

Gnomad EAS AF: 0.0344

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.0193

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0322

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.121 AC: 18413 AN: 152116 Hom.: 2418 Cov.: 32 AF XY: 0.120 AC XY: 8901 AN XY: 74366

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.0895

Gnomad4 ASJ AF: 0.0395

Gnomad4 EAS AF: 0.0344

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.0193

Gnomad4 NFE AF: 0.0322

Gnomad4 OTH AF: 0.117

Alfa AF: 0.111 Hom.: 321

Bravo AF: 0.133

Asia WGS AF: 0.132 AC: 460 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Nov 12, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.1
DANN	Benign	0.77

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

Publications

LitVar

Other links and lift over

dbSNP: rs12079868; hg19: chr1-24691137;