rs544669429

Variant names:

• chr9-137253370-GATGCACCCTTCTGGCTGGCCAACCCTTCT-G
• rs544669429
• ENST00000388931.7:c.1072_1100delCACCCTTCTGGCTGGCCAACCCTTCTATG

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BS1 BS2

The NM_001256699.2(STPG3):​c.1072_1100delCACCCTTCTGGCTGGCCAACCCTTCTATG​(p.His358GlyfsTer27) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00294 in 1,534,214 control chromosomes in the GnomAD database, including 68 homozygotes. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0038 (6 hom., cov: 33)
  • Exomes 𝑓: 0.0028 (62 hom.)
• Consequence: STPG3 NM_001256699.2 frameshift
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0980
• Publications: 3 publications found

Genes affected

STPG3 (HGNC:37285): (sperm-tail PG-rich repeat containing 3) Predicted to be active in cytoskeleton. [provided by Alliance of Genome Resources, Apr 2022]

CIMIP2A (HGNC:33818): (ciliary microtubule inner protein 2A) Located in ciliary basal body. [provided by Alliance of Genome Resources, Apr 2022]

STPG3-AS1 (HGNC:51176): (STPG3 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP6: Variant 9-137253370-GATGCACCCTTCTGGCTGGCCAACCCTTCT-G is Benign according to our data. Variant chr9-137253370-GATGCACCCTTCTGGCTGGCCAACCCTTCT-G is described in ClinVar as Benign. ClinVar VariationId is 732859.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.00375 (571/152246) while in subpopulation EAS AF = 0.0313 (162/5180). AF 95% confidence interval is 0.0273. There are 6 homozygotes in GnomAd4. There are 345 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 6 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001256699.2. 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
	STPG3	NM_001004353.4	MANE Select	c.*129_*157delCACCCTTCTGGCTGGCCAACCCTTCTATG		3_prime_UTR	Exon 6 of 6	NP_001004353.2	Q8N7X2-4
	STPG3	NM_001256699.2		c.1072_1100delCACCCTTCTGGCTGGCCAACCCTTCTATG	p.His358GlyfsTer27	frameshift	Exon 6 of 6	NP_001243628.1	Q8N7X2-2
	STPG3	NM_001256700.2		c.907_935delCACCCTTCTGGCTGGCCAACCCTTCTATG	p.His303GlyfsTer27	frameshift	Exon 6 of 6	NP_001243629.1	Q8N7X2-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STPG3	ENST00000388931.7	TSL:1	c.1072_1100delCACCCTTCTGGCTGGCCAACCCTTCTATG	p.His358GlyfsTer27	frameshift	Exon 6 of 6	ENSP00000373583.3	Q8N7X2-2
	STPG3	ENST00000611378.4	TSL:1	c.907_935delCACCCTTCTGGCTGGCCAACCCTTCTATG	p.His303GlyfsTer26	frameshift	Exon 6 of 6	ENSP00000477998.1	Q8N7X2-3
	STPG3	ENST00000412566.6	TSL:1 MANE Select	c.*129_*157delCACCCTTCTGGCTGGCCAACCCTTCTATG		3_prime_UTR	Exon 6 of 6	ENSP00000391218.1	Q8N7X2-4

Frequencies

GnomAD3 genomes AF: 0.00376 AC: 572 AN: 152128 Hom.: 6 Cov.: 33

Gnomad AFR AF: 0.0000483

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000131

Gnomad ASJ AF: 0.0150

Gnomad EAS AF: 0.0314

Gnomad SAS AF: 0.00456

Gnomad FIN AF: 0.0257

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000809

Gnomad OTH AF: 0.000956

GnomAD2 exomes AF: 0.00572 AC: 783 AN: 136958 AF XY: 0.00554

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000864

Gnomad ASJ exome AF: 0.0148

Gnomad EAS exome AF: 0.0333

Gnomad FIN exome AF: 0.0231

Gnomad NFE exome AF: 0.000616

Gnomad OTH exome AF: 0.00638

GnomAD4 exome AF: 0.00285 AC: 3937 AN: 1381968 Hom.: 62 AF XY: 0.00283 AC XY: 1931 AN XY: 681384

African (AFR) AF: 0.0000319 AC: 1 AN: 31306

American (AMR) AF: 0.0000582 AC: 2 AN: 34376

Ashkenazi Jewish (ASJ) AF: 0.0171 AC: 421 AN: 24588

East Asian (EAS) AF: 0.0488 AC: 1739 AN: 35628

South Asian (SAS) AF: 0.00156 AC: 122 AN: 78390

European-Finnish (FIN) AF: 0.0257 AC: 1031 AN: 40128

Middle Eastern (MID) AF: 0.000708 AC: 4 AN: 5652

European-Non Finnish (NFE) AF: 0.000394 AC: 423 AN: 1074356

Other (OTH) AF: 0.00337 AC: 194 AN: 57544

GnomAD4 genome AF: 0.00375 AC: 571 AN: 152246 Hom.: 6 Cov.: 33 AF XY: 0.00463 AC XY: 345 AN XY: 74452

African (AFR) AF: 0.0000481 AC: 2 AN: 41552

American (AMR) AF: 0.000131 AC: 2 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0150 AC: 52 AN: 3470

East Asian (EAS) AF: 0.0313 AC: 162 AN: 5180

South Asian (SAS) AF: 0.00456 AC: 22 AN: 4824

European-Finnish (FIN) AF: 0.0257 AC: 273 AN: 10608

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.000809 AC: 55 AN: 67996

Other (OTH) AF: 0.000946 AC: 2 AN: 2114

Alfa AF: 0.00309 Hom.: 0

Bravo AF: 0.00219

Asia WGS AF: 0.0140 AC: 47 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.098
Mutation Taster		=189/11	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs544669429; hg19: chr9-140147822; COSMIC: COSV58023720; COSMIC: COSV58023720;