rs7691268

Variant names:

• chr4-97312809-A-G
• rs7691268
• ENST00000522676.5:c.463-124976T>C

Variant summary

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

The ENST00000522676.5(STPG2):​c.463-124976T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0658 in 152,130 control chromosomes in the GnomAD database, including 438 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 0.066 (438 hom., cov: 32)
• Consequence: STPG2 ENST00000522676.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221
• 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000522676.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STPG2	ENST00000522676.5	TSL:1	c.463-124976T>C		intron	N/A	ENSP00000428346.1	H0YAZ7
	STPG2	ENST00000506482.1	TSL:4	n.269-49228T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0658 AC: 10000 AN: 152012 Hom.: 435 Cov.: 32

Gnomad AFR AF: 0.0239

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.0424

Gnomad EAS AF: 0.0870

Gnomad SAS AF: 0.0585

Gnomad FIN AF: 0.0943

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0697

Gnomad OTH AF: 0.0799

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

GnomAD4 genome AF: 0.0658 AC: 10015 AN: 152130 Hom.: 438 Cov.: 32 AF XY: 0.0683 AC XY: 5080 AN XY: 74366

African (AFR) AF: 0.0240 AC: 996 AN: 41552

American (AMR) AF: 0.139 AC: 2127 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0424 AC: 147 AN: 3466

East Asian (EAS) AF: 0.0870 AC: 447 AN: 5136

South Asian (SAS) AF: 0.0588 AC: 284 AN: 4830

European-Finnish (FIN) AF: 0.0943 AC: 1000 AN: 10608

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0697 AC: 4736 AN: 67966

Other (OTH) AF: 0.0829 AC: 175 AN: 2112

Alfa AF: 0.0666 Hom.: 213

Bravo AF: 0.0690

Asia WGS AF: 0.0750 AC: 261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.0
DANN	Benign	0.51
PhyloP100		0.22

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7691268;

hg19: chr4-98233960;