rs969049

Variant names:

• chr4-98067706-C-T
• rs969049
• NM_174952.3:c.612+38247G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_174952.3(STPG2):​c.612+38247G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 151,914 control chromosomes in the GnomAD database, including 12,374 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 0.40 (12374 hom., cov: 32)
• Consequence: STPG2 NM_174952.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 2 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.458 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STPG2	NM_174952.3	MANE Select	c.612+38247G>A		intron	N/A	NP_777612.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STPG2	ENST00000295268.4	TSL:1 MANE Select	c.612+38247G>A		intron	N/A	ENSP00000295268.3

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60639 AN: 151798 Hom.: 12369 Cov.: 32

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.399 AC: 60665 AN: 151914 Hom.: 12374 Cov.: 32 AF XY: 0.393 AC XY: 29195 AN XY: 74266

African (AFR) AF: 0.463 AC: 19207 AN: 41442

American (AMR) AF: 0.320 AC: 4882 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1052 AN: 3464

East Asian (EAS) AF: 0.284 AC: 1467 AN: 5170

South Asian (SAS) AF: 0.432 AC: 2079 AN: 4812

European-Finnish (FIN) AF: 0.301 AC: 3171 AN: 10542

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.403 AC: 27371 AN: 67930

Other (OTH) AF: 0.393 AC: 826 AN: 2100

Alfa AF: 0.394 Hom.: 1557

Bravo AF: 0.402

Asia WGS AF: 0.387 AC: 1341 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.66
PhyloP100		-1.2
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: rs969049; hg19: chr4-98988857;