rs408067

chr17-2303942-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000572709.5(SRR):c.-5+465C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.52 in 298,110 control chromosomes in the GnomAD database, including 44,037 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 0.54 (23449 hom., cov: 32)
  • Exomes 𝑓: 0.50 (20588 hom.)
• Consequence: SRR ENST00000572709.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.466

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SRR	XM_006721565.4	c.-5+465C>G		intron_variant
SRR	NM_021947.3			upstream_gene_variant		ENST00000344595.10
SRR	NM_001304803.1			upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SRR	ENST00000344595.10			upstream_gene_variant		1	NM_021947.3	P1

Frequencies

GnomAD3 genomes AF: 0.542 AC: 82193 AN: 151606 Hom.: 23438 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.653

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.558

GnomAD4 exome AF: 0.498 AC: 72926 AN: 146396 Hom.: 20588 Cov.: 2 AF XY: 0.502 AC XY: 39970 AN XY: 79672

Gnomad4 AFR exome AF: 0.184

Gnomad4 AMR exome AF: 0.389

Gnomad4 ASJ exome AF: 0.529

Gnomad4 EAS exome AF: 0.577

Gnomad4 SAS exome AF: 0.556

Gnomad4 FIN exome AF: 0.474

Gnomad4 NFE exome AF: 0.502

Gnomad4 OTH exome AF: 0.461

GnomAD4 genome AF: 0.542 AC: 82236 AN: 151714 Hom.: 23449 Cov.: 32 AF XY: 0.545 AC XY: 40420 AN XY: 74146

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.596

Gnomad4 ASJ AF: 0.653

Gnomad4 EAS AF: 0.691

Gnomad4 SAS AF: 0.546

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.612

Gnomad4 OTH AF: 0.558

Alfa AF: 0.571 Hom.: 3099

Bravo AF: 0.534

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
Dann	Benign	0.87

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

LitVar

Other links and lift over

dbSNP: rs408067; hg19: chr17-2207236;