dbSNP rs12763: SURF2:p.Gly213Ser (chr9-133360384-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_017503.5(SURF2):c.637G>A(p.Gly213Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 1,612,964 control chromosomes in the GnomAD database, including 121,454 homozygotes. In-silico tool predicts a benign outcome for this variant. 5/6 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.33 ( 9154 hom., cov: 33)

Exomes 𝑓: 0.39 ( 112300 hom. )

Consequence

SURF2
NM_017503.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0870

Publications

51 publications found

Variant links:

Genes affected

SURF2 (HGNC:11475): (surfeit 2) This gene shares a bidirectional promoter with surfeit 1 (SURF1; GeneID: 6834), which is located on the opposite strand. It encodes a conserved protein that is expressed in a variety of tissues. [provided by RefSeq, Jul 2013]

SURF2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (MetaRNN=0.0023717284).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SURF2	NM_017503.5 link	c.637G>A	p.Gly213Ser	missense_variant	Exon 5 of 6	ENST00000371964.5	NP_059973.4
SURF2	NM_001278928.2 link	c.637G>A	p.Gly213Ser	missense_variant	Exon 5 of 6		NP_001265857.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SURF2	ENST00000371964.5 link	c.637G>A	p.Gly213Ser	missense_variant	Exon 5 of 6	1	NM_017503.5	ENSP00000361032.4

Frequencies

GnomAD3 genomes

AF:

0.333

AC:

50582

AN:

151944

Hom.:

9148

Cov.:

show subpopulations

Gnomad AFR

AF:

0.206

Gnomad AMI

AF:

0.295

Gnomad AMR

AF:

0.326

Gnomad ASJ

AF:

0.263

Gnomad EAS

AF:

0.323

Gnomad SAS

AF:

0.466

Gnomad FIN

AF:

0.460

Gnomad MID

AF:

0.237

Gnomad NFE

AF:

0.389

Gnomad OTH

AF:

0.307

GnomAD4 exome

AF:

0.388

AC:

566908

AN:

1460902

Hom.:

112300

Cov.:

AF XY:

0.391

AC XY:

284046

AN XY:

726702

show subpopulations

African (AFR)

AF:

0.204

AC:

6840

AN:

33474

American (AMR)

AF:

0.373

AC:

16629

AN:

44632

Ashkenazi Jewish (ASJ)

AF:

0.266

AC:

6953

AN:

26136

East Asian (EAS)

AF:

0.319

AC:

12644

AN:

39682

South Asian (SAS)

AF:

0.465

AC:

40071

AN:

86230

European-Finnish (FIN)

AF:

0.470

AC:

24838

AN:

52804

Middle Eastern (MID)

AF:

0.271

AC:

1559

AN:

5762

European-Non Finnish (NFE)

AF:

0.392

AC:

435279

AN:

1111810

Other (OTH)

AF:

0.366

AC:

22095

AN:

60372

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.526

Heterozygous variant carriers

22613

45225

67838

90450

113063

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

13556

27112

40668

54224

67780

<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:

0.333

AC:

50586

AN:

152062

Hom.:

9154

Cov.:

AF XY:

0.337

AC XY:

25078

AN XY:

74308

show subpopulations

African (AFR)

AF:

0.205

AC:

8507

AN:

41494

American (AMR)

AF:

0.326

AC:

4985

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.263

AC:

913

AN:

3470

East Asian (EAS)

AF:

0.322

AC:

1663

AN:

5158

South Asian (SAS)

AF:

0.467

AC:

2251

AN:

4824

European-Finnish (FIN)

AF:

0.460

AC:

4848

AN:

10546

Middle Eastern (MID)

AF:

0.248

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.389

AC:

26434

AN:

67960

Other (OTH)

AF:

0.305

AC:

643

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1670

3340

5011

6681

8351

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

518

1036

1554

2072

2590

<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:

0.373

Hom.:

6642

Bravo

AF:

0.311

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.078

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.4

(source)

MetaRNN

Benign

0.0024

PhyloP100

0.087

Sift4G

Benign

1.0

Vest4

0.043

gMVP

0.052

Splicing

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