Genetic Variant NM_001166293.2:c.1389+418T>C (chr1-84655414-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NM_001166293.2(SSX2IP):c.1389+418T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0193 in 1,288,222 control chromosomes in the GnomAD database, including 293 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 0.017 ( 32 hom., cov: 31)

Exomes 𝑓: 0.020 ( 261 hom. )

Consequence

SSX2IP
NM_001166293.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.13

Publications

0 publications found

Variant links:

Genes affected

SSX2IP (HGNC:16509): (SSX family member 2 interacting protein) This gene encodes a protein that binds the cancer-testis antigen Synovial Sarcoma X breakpoint 2 protein. The encoded protein may regulate the activity of Synovial Sarcoma X breakpoint 2 protein in malignant cells. Alternate splicing results in multiple transcript variants. A pseudogene of this gene is found on chromosome 3. [provided by RefSeq, Oct 2009]

SSX2IP links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.017 (2588/152182) while in subpopulation NFE AF = 0.022 (1497/67976). AF 95% confidence interval is 0.0211. There are 32 homozygotes in GnomAd4. There are 1341 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 32 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SSX2IP	NM_001166293.2 link	c.1389+418T>C		intron_variant	Intron 11 of 13	ENST00000342203.8	NP_001159765.1	Q9Y2D8-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SSX2IP	ENST00000342203.8 link	c.1389+418T>C		intron_variant	Intron 11 of 13	1	NM_001166293.2	ENSP00000340279.3		Q9Y2D8-1
SSX2IP	ENST00000476905.6 link	n.1501+51T>C		intron_variant	Intron 13 of 15	2		ENSP00000474925.1		S4R403

Frequencies

GnomAD3 genomes

AF:

0.0170

AC:

2589

AN:

152064

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00316

Gnomad AMI

AF:

0.00548

Gnomad AMR

AF:

0.0163

Gnomad ASJ

AF:

0.0216

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00829

Gnomad FIN

AF:

0.0509

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.0220

Gnomad OTH

AF:

0.0201

GnomAD4 exome

AF:

0.0196

AC:

22284

AN:

1136040

Hom.:

261

Cov.:

AF XY:

0.0192

AC XY:

10725

AN XY:

557154

show subpopulations

African (AFR)

AF:

0.00353

AC:

AN:

24344

American (AMR)

AF:

0.0108

AC:

304

AN:

28072

Ashkenazi Jewish (ASJ)

AF:

0.0196

AC:

312

AN:

15888

East Asian (EAS)

AF:

0.000156

AC:

AN:

12840

South Asian (SAS)

AF:

0.00713

AC:

539

AN:

75618

European-Finnish (FIN)

AF:

0.0524

AC:

666

AN:

12714

Middle Eastern (MID)

AF:

0.0467

AC:

203

AN:

4350

European-Non Finnish (NFE)

AF:

0.0211

AC:

19415

AN:

920752

Other (OTH)

AF:

0.0183

AC:

757

AN:

41462

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1181

2362

3543

4724

5905

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

814

1628

2442

3256

4070

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0170

AC:

2588

AN:

152182

Hom.:

Cov.:

AF XY:

0.0180

AC XY:

1341

AN XY:

74398

show subpopulations

African (AFR)

AF:

0.00315

AC:

131

AN:

41548

American (AMR)

AF:

0.0163

AC:

249

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.0216

AC:

AN:

3466

East Asian (EAS)

AF:

0.000193

AC:

AN:

5180

South Asian (SAS)

AF:

0.00830

AC:

AN:

4822

European-Finnish (FIN)

AF:

0.0509

AC:

539

AN:

10592

Middle Eastern (MID)

AF:

0.0306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0220

AC:

1497

AN:

67976

Other (OTH)

AF:

0.0199

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

128

255

383

510

638

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

128

160

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0183

Hom.:

Bravo

AF:

0.0141

Asia WGS

AF:

0.00404

AC:

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.055

(source)

DANN

Benign

0.67

PhyloP100

-1.1

Mutation Taster

=100/0

polymorphism

(source)

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over