dbSNP rs1729659: SANBR:p.Lys216Lys (chr2-61077136-A-G) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001129993.3(SANBR):c.648A>G(p.Lys216Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 1,606,506 control chromosomes in the GnomAD database, including 85,568 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 0.33 ( 8913 hom., cov: 32)

Exomes 𝑓: 0.32 ( 76655 hom. )

Consequence

SANBR
NM_001129993.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.399

Publications

15 publications found

Variant links:

Genes affected

SANBR (HGNC:29387): (SANT and BTB domain regulator of CSR)

SANBR links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.55).

BP7

Synonymous conserved (PhyloP=0.399 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SANBR	NM_001129993.3 link	c.648A>G	p.Lys216Lys	synonymous_variant	Exon 6 of 22	ENST00000402291.6	NP_001123465.1	Q6NSI8-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SANBR	ENST00000402291.6 link	c.648A>G	p.Lys216Lys	synonymous_variant	Exon 6 of 22	1	NM_001129993.3	ENSP00000385579.1		Q6NSI8-1

Frequencies

GnomAD3 genomes

AF:

0.335

AC:

50844

AN:

151940

Hom.:

8890

Cov.:

show subpopulations

Gnomad AFR

AF:

0.378

Gnomad AMI

AF:

0.434

Gnomad AMR

AF:

0.377

Gnomad ASJ

AF:

0.385

Gnomad EAS

AF:

0.419

Gnomad SAS

AF:

0.206

Gnomad FIN

AF:

0.216

Gnomad MID

AF:

0.351

Gnomad NFE

AF:

0.315

Gnomad OTH

AF:

0.362

GnomAD2 exomes

AF:

0.329

AC:

82114

AN:

249920

AF XY:

0.321

show subpopulations

Gnomad AFR exome

AF:

0.382

Gnomad AMR exome

AF:

0.404

Gnomad ASJ exome

AF:

0.382

Gnomad EAS exome

AF:

0.435

Gnomad FIN exome

AF:

0.227

Gnomad NFE exome

AF:

0.323

Gnomad OTH exome

AF:

0.336

GnomAD4 exome

AF:

0.320

AC:

466034

AN:

1454448

Hom.:

76655

Cov.:

AF XY:

0.317

AC XY:

229437

AN XY:

723828

show subpopulations

African (AFR)

AF:

0.382

AC:

12719

AN:

33336

American (AMR)

AF:

0.402

AC:

17915

AN:

44574

Ashkenazi Jewish (ASJ)

AF:

0.384

AC:

10000

AN:

26060

East Asian (EAS)

AF:

0.434

AC:

17215

AN:

39632

South Asian (SAS)

AF:

0.225

AC:

19242

AN:

85636

European-Finnish (FIN)

AF:

0.225

AC:

12034

AN:

53404

Middle Eastern (MID)

AF:

0.320

AC:

1839

AN:

5744

European-Non Finnish (NFE)

AF:

0.321

AC:

355122

AN:

1105886

Other (OTH)

AF:

0.331

AC:

19948

AN:

60176

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

15292

30584

45876

61168

76460

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11642

23284

34926

46568

58210

<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:

0.335

AC:

50919

AN:

152058

Hom.:

8913

Cov.:

AF XY:

0.330

AC XY:

24517

AN XY:

74346

show subpopulations

African (AFR)

AF:

0.379

AC:

15708

AN:

41464

American (AMR)

AF:

0.377

AC:

5754

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.385

AC:

1338

AN:

3472

East Asian (EAS)

AF:

0.419

AC:

2171

AN:

5178

South Asian (SAS)

AF:

0.205

AC:

992

AN:

4830

European-Finnish (FIN)

AF:

0.216

AC:

2281

AN:

10566

Middle Eastern (MID)

AF:

0.344

AC:

101

AN:

294

European-Non Finnish (NFE)

AF:

0.315

AC:

21419

AN:

67970

Other (OTH)

AF:

0.361

AC:

761

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1716

3433

5149

6866

8582

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

494

988

1482

1976

2470

<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:

0.331

Hom.:

18913

Bravo

AF:

0.356

Asia WGS

AF:

0.296

AC:

1031

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

7.4

(source)

DANN

Benign

0.67

PhyloP100

0.40

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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