4-97892967-A-G

Variant names:

• chr4-97892967-A-G
• rs10026181
• NM_174952.3:c.1044+50930T>C

Variant summary

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

The NM_174952.3(STPG2):​c.1044+50930T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 152,134 control chromosomes in the GnomAD database, including 5,281 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 0.24 (5277 hom., cov: 32)
  • Exomes 𝑓: 0.42 (4 hom.)
• Consequence: STPG2 NM_174952.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.439

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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STPG2	NM_174952.3	c.1044+50930T>C		intron_variant	Intron 8 of 10	ENST00000295268.4	NP_777612.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STPG2	ENST00000295268.4	c.1044+50930T>C		intron_variant	Intron 8 of 10	1	NM_174952.3	ENSP00000295268.3
STPG2	ENST00000522676.5	c.186+50930T>C		intron_variant	Intron 2 of 4	1		ENSP00000428346.1
STPG2	ENST00000506482.1	n.152+85T>C		intron_variant	Intron 1 of 4	4

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36945 AN: 151992 Hom.: 5275 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.256

GnomAD4 exome AF: 0.417 AC: 10 AN: 24 Hom.: 4 AF XY: 0.444 AC XY: 8 AN XY: 18

Gnomad4 AFR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.00

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.438

GnomAD4 genome AF: 0.243 AC: 36955 AN: 152110 Hom.: 5277 Cov.: 32 AF XY: 0.240 AC XY: 17823 AN XY: 74360

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.254

Alfa AF: 0.128 Hom.: 240

Bravo AF: 0.235

Asia WGS AF: 0.163 AC: 568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.6
DANN	Benign	0.45

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: rs10026181; hg19: chr4-98814118;