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

Variant summary

Our verdict is . The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001166293.2(SSX2IP):c.1389+418T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000088 in 1,136,074 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 31)

Exomes 𝑓: 8.8e-7 ( 0 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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new If you want to explore the variant's impact on the transcript NM_001166293.2, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001166293.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SSX2IP	NM_001166293.2	MANE Select	c.1389+418T>G	intron	N/A	NP_001159765.1	Q9Y2D8-1
SSX2IP	NM_001166417.2		c.1389+418T>G	intron	N/A	NP_001159889.1	Q9Y2D8-1
SSX2IP	NM_014021.4		c.1389+418T>G	intron	N/A	NP_054740.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SSX2IP	ENST00000342203.8	TSL:1 MANE Select	c.1389+418T>G	intron	N/A	ENSP00000340279.3	Q9Y2D8-1
SSX2IP	ENST00000603677.1	TSL:1	c.-54-3417T>G	intron	N/A	ENSP00000473763.1	S4R2Y6
SSX2IP	ENST00000476905.6	TSL:2	n.1501+51T>G	intron	N/A	ENSP00000474925.1	S4R403

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

8.80e-7

AC:

AN:

1136074

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

557170

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

24344

American (AMR)

AF:

0.00

AC:

AN:

28072

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

15888

East Asian (EAS)

AF:

0.00

AC:

AN:

12840

South Asian (SAS)

AF:

0.00

AC:

AN:

75620

European-Finnish (FIN)

AF:

0.00

AC:

AN:

12716

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4354

European-Non Finnish (NFE)

AF:

0.00000109

AC:

AN:

920778

Other (OTH)

AF:

0.00

AC:

AN:

41462

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.575

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.017

(source)

DANN

Benign

0.65

PhyloP100

-1.1

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

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over