Genetic Variant SGSM2:c.2803-217T>G (chr17-2377640-T-G) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

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

The NM_014853.3(SGSM2):c.2803-217T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000335 in 298,662 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: 30)

Exomes 𝑓: 0.0000033 ( 0 hom. )

Consequence

SGSM2
NM_014853.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.148

Publications

8 publications found

Variant links:

Genes affected

SGSM2 (HGNC:29026): (small G protein signaling modulator 2) The protein encoded by this gene is a GTPase activator with activity towards RAB32 and RAB33B, which are regulators of membrane trafficking. The encoded protein inactivates RAB32 and can bind RAB9A-GTP, a protein required for RAB32 activation. [provided by RefSeq, Oct 2016]

SGSM2 links:

SGSM2-AS1 (HGNC:56091): (SGSM2 antisense RNA 1)

SGSM2-AS1 links:

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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=-0.69).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SGSM2	NM_014853.3 link	c.2803-217T>G		intron_variant	Intron 21 of 23	ENST00000268989.8	NP_055668.2	O43147-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SGSM2	ENST00000268989.8 link	c.2803-217T>G		intron_variant	Intron 21 of 23	1	NM_014853.3	ENSP00000268989.3		O43147-2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000335

AC:

AN:

298662

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

157862

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

8670

American (AMR)

AF:

0.00

AC:

AN:

11050

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

9174

East Asian (EAS)

AF:

0.00

AC:

AN:

20680

South Asian (SAS)

AF:

0.00

AC:

AN:

32098

European-Finnish (FIN)

AF:

0.00

AC:

AN:

17482

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1344

European-Non Finnish (NFE)

AF:

0.00000553

AC:

AN:

180890

Other (OTH)

AF:

0.00

AC:

AN:

17274

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

86870

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

5.9

(source)

DANN

Benign

0.74

PhyloP100

0.15

PromoterAI

-0.00080

Neutral

(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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over