4-97892967-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_174952.3. 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
	STPG2	NM_174952.3	MANE Select	c.1044+50930T>C		intron	N/A	NP_777612.1	Q8N412

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STPG2	ENST00000295268.4	TSL:1 MANE Select	c.1044+50930T>C		intron	N/A	ENSP00000295268.3	Q8N412
	STPG2	ENST00000522676.5	TSL:1	c.186+50930T>C		intron	N/A	ENSP00000428346.1	H0YAZ7
	STPG2	ENST00000506482.1	TSL:4	n.152+85T>C		intron	N/A

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

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.438 AC: 7 AN: 16

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.100 AC: 4169 AN: 41550

American (AMR) AF: 0.233 AC: 3561 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 723 AN: 3468

East Asian (EAS) AF: 0.170 AC: 876 AN: 5164

South Asian (SAS) AF: 0.199 AC: 958 AN: 4824

European-Finnish (FIN) AF: 0.282 AC: 2985 AN: 10570

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22643 AN: 67950

Other (OTH) AF: 0.254 AC: 537 AN: 2112

Alfa AF: 0.126 Hom.: 247

Bravo AF: 0.235

Asia WGS AF: 0.163 AC: 568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.6
DANN	Benign	0.45
PhyloP100		-0.44
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10026181; hg19: chr4-98814118;