chr4-98044545-T-C

Position:

• chr4-98044545-T-C

Variant summary

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

The NM_174952.3(STPG2):​c.612+61408A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0643 in 152,178 control chromosomes in the GnomAD database, including 414 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 0.064 (414 hom., cov: 32)
• Consequence: STPG2 NM_174952.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780

Genes affected

STPG2 (HGNC:28712): (sperm tail PG-rich repeat containing 2)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STPG2	NM_174952.3	c.612+61408A>G		intron_variant		ENST00000295268.4	NP_777612.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STPG2	ENST00000295268.4	c.612+61408A>G		intron_variant		1	NM_174952.3	ENSP00000295268	P1

Frequencies

GnomAD3 genomes AF: 0.0644 AC: 9791 AN: 152060 Hom.: 417 Cov.: 32

Gnomad AFR AF: 0.0641

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.0486

Gnomad ASJ AF: 0.0997

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.0190

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0581

Gnomad OTH AF: 0.0709

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

GnomAD4 genome AF: 0.0643 AC: 9785 AN: 152178 Hom.: 414 Cov.: 32 AF XY: 0.0648 AC XY: 4818 AN XY: 74406

Gnomad4 AFR AF: 0.0639

Gnomad4 AMR AF: 0.0485

Gnomad4 ASJ AF: 0.0997

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.0190

Gnomad4 NFE AF: 0.0581

Gnomad4 OTH AF: 0.0702

Alfa AF: 0.0625 Hom.: 483

Bravo AF: 0.0635

Asia WGS AF: 0.165 AC: 573 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	8.3
DANN	Benign	0.62

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs7677523; hg19: chr4-98965696; COSMIC: COSV54784683; COSMIC: COSV54784683;