chr4-97306224-G-T

Variant names:

• chr4-97306224-G-T
• rs13119820
• ENST00000522676.5:c.463-118391C>A

Variant summary

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

The ENST00000522676.5(STPG2):​c.463-118391C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 151,650 control chromosomes in the GnomAD database, including 14,222 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 0.43 (14222 hom., cov: 32)
• Consequence: STPG2 ENST00000522676.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.399
• Publications: 1 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.508 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STPG2	ENST00000522676.5	TSL:1	c.463-118391C>A		intron	N/A	ENSP00000428346.1
	STPG2	ENST00000506482.1	TSL:4	n.269-42643C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64671 AN: 151532 Hom.: 14190 Cov.: 32

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.427 AC: 64756 AN: 151650 Hom.: 14222 Cov.: 32 AF XY: 0.427 AC XY: 31666 AN XY: 74094

African (AFR) AF: 0.513 AC: 21246 AN: 41380

American (AMR) AF: 0.477 AC: 7239 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1127 AN: 3466

East Asian (EAS) AF: 0.455 AC: 2321 AN: 5104

South Asian (SAS) AF: 0.507 AC: 2447 AN: 4826

European-Finnish (FIN) AF: 0.288 AC: 3036 AN: 10540

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25847 AN: 67848

Other (OTH) AF: 0.432 AC: 910 AN: 2106

Alfa AF: 0.401 Hom.: 38984

Bravo AF: 0.445

Asia WGS AF: 0.502 AC: 1744 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.54
DANN	Benign	0.42
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs13119820; hg19: chr4-98227375;