Genetic Variant SRR:c.399+102C>T (chr17-2319031-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_021947.3(SRR):c.399+102C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 734,066 control chromosomes in the GnomAD database, including 66,584 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 0.46 ( 16649 hom., cov: 30)

Exomes 𝑓: 0.40 ( 49935 hom. )

Consequence

SRR
NM_021947.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.184

Publications

16 publications found

Variant links:

Genes affected

SRR (HGNC:14398): (serine racemase) Enables several functions, including L-serine ammonia-lyase activity; PDZ domain binding activity; and anion binding activity. Involved in pyruvate biosynthetic process; response to lipopolysaccharide; and serine family amino acid metabolic process. Located in cytoplasm and neuronal cell body. [provided by Alliance of Genome Resources, Apr 2022]

SRR 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=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021947.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SRR	NM_021947.3	MANE Select	c.399+102C>T		intron	N/A	NP_068766.1	Q9GZT4
	SRR	NM_001304803.1		c.-49+102C>T		intron	N/A	NP_001291732.1	Q3ZK31

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SRR	ENST00000344595.10	TSL:1 MANE Select	c.399+102C>T	intron	N/A	ENSP00000339435.5	Q9GZT4
SRR	ENST00000909632.1		c.399+102C>T	intron	N/A	ENSP00000579691.1
SRR	ENST00000909633.1		c.399+102C>T	intron	N/A	ENSP00000579692.1

Frequencies

GnomAD3 genomes

AF:

0.456

AC:

69226

AN:

151696

Hom.:

16624

Cov.:

show subpopulations

Gnomad AFR

AF:

0.581

Gnomad AMI

AF:

0.510

Gnomad AMR

AF:

0.491

Gnomad ASJ

AF:

0.409

Gnomad EAS

AF:

0.665

Gnomad SAS

AF:

0.305

Gnomad FIN

AF:

0.424

Gnomad MID

AF:

0.370

Gnomad NFE

AF:

0.375

Gnomad OTH

AF:

0.454

GnomAD4 exome

AF:

0.400

AC:

232617

AN:

582252

Hom.:

49935

AF XY:

0.391

AC XY:

121969

AN XY:

311926

show subpopulations

African (AFR)

AF:

0.577

AC:

8373

AN:

14502

American (AMR)

AF:

0.519

AC:

14104

AN:

27152

Ashkenazi Jewish (ASJ)

AF:

0.423

AC:

6659

AN:

15728

East Asian (EAS)

AF:

0.697

AC:

22292

AN:

31974

South Asian (SAS)

AF:

0.289

AC:

16111

AN:

55774

European-Finnish (FIN)

AF:

0.420

AC:

19455

AN:

46286

Middle Eastern (MID)

AF:

0.401

AC:

1272

AN:

3176

European-Non Finnish (NFE)

AF:

0.369

AC:

132079

AN:

358302

Other (OTH)

AF:

0.418

AC:

12272

AN:

29358

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

6188

12376

18564

24752

30940

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1846

3692

5538

7384

9230

<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:

0.457

AC:

69313

AN:

151814

Hom.:

16649

Cov.:

AF XY:

0.458

AC XY:

33968

AN XY:

74202

show subpopulations

African (AFR)

AF:

0.582

AC:

24063

AN:

41380

American (AMR)

AF:

0.491

AC:

7480

AN:

15238

Ashkenazi Jewish (ASJ)

AF:

0.409

AC:

1419

AN:

3468

East Asian (EAS)

AF:

0.666

AC:

3426

AN:

5148

South Asian (SAS)

AF:

0.307

AC:

1477

AN:

4818

European-Finnish (FIN)

AF:

0.424

AC:

4459

AN:

10522

Middle Eastern (MID)

AF:

0.378

AC:

111

AN:

294

European-Non Finnish (NFE)

AF:

0.375

AC:

25458

AN:

67926

Other (OTH)

AF:

0.453

AC:

957

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1838

3676

5513

7351

9189

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

614

1228

1842

2456

3070

<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:

0.407

Hom.:

49932

Bravo

AF:

0.470

Asia WGS

AF:

0.478

AC:

1662

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

3.1

(source)

DANN

Benign

0.27

PhyloP100

-0.18

Mutation Taster

=100/0

polymorphism (auto)

(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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over