4-97349649-T-C

Variant names:

• chr4-97349649-T-C
• rs1462767
• ENST00000522676.5:c.463-161816A>G

Variant summary

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

The ENST00000522676.5(STPG2):​c.463-161816A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 151,834 control chromosomes in the GnomAD database, including 18,236 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 0.47 (18236 hom., cov: 31)
• Consequence: STPG2 ENST00000522676.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.239
• Publications: 0 publications found

Genes affected

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

ENSG00000254044 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STPG2	ENST00000522676.5	c.463-161816A>G		intron_variant	Intron 4 of 4	1		ENSP00000428346.1
STPG2	ENST00000506482.1	n.269-86068A>G		intron_variant	Intron 2 of 4	4
ENSG00000254044	ENST00000521680.5	n.422-14936A>G		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.474 AC: 71899 AN: 151714 Hom.: 18201 Cov.: 31

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.474 AC: 71992 AN: 151834 Hom.: 18236 Cov.: 31 AF XY: 0.473 AC XY: 35092 AN XY: 74198

African (AFR) AF: 0.656 AC: 27172 AN: 41428

American (AMR) AF: 0.500 AC: 7602 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1135 AN: 3464

East Asian (EAS) AF: 0.466 AC: 2389 AN: 5132

South Asian (SAS) AF: 0.524 AC: 2524 AN: 4816

European-Finnish (FIN) AF: 0.297 AC: 3133 AN: 10556

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.389 AC: 26446 AN: 67928

Other (OTH) AF: 0.471 AC: 991 AN: 2104

Alfa AF: 0.414 Hom.: 56353

Bravo AF: 0.497

Asia WGS AF: 0.514 AC: 1787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.86
DANN	Benign	0.37
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs1462767; hg19: chr4-98270800;