rs391300

Positions:

• chr17-2312964-T-C

Variant summary

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

The NM_021947.3(SRR):​c.-4-2593T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.584 in 151,994 control chromosomes in the GnomAD database, including 26,302 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 0.58 (26302 hom., cov: 31)
• Consequence: SRR NM_021947.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.369

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=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SRR	NM_021947.3	c.-4-2593T>C		intron_variant		ENST00000344595.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SRR	ENST00000344595.10	c.-4-2593T>C		intron_variant		1	NM_021947.3	P1

Frequencies

GnomAD3 genomes AF: 0.584 AC: 88669 AN: 151876 Hom.: 26283 Cov.: 31

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.584

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.584 AC: 88736 AN: 151994 Hom.: 26302 Cov.: 31 AF XY: 0.585 AC XY: 43438 AN XY: 74284

Gnomad4 AFR AF: 0.480

Gnomad4 AMR AF: 0.612

Gnomad4 ASJ AF: 0.644

Gnomad4 EAS AF: 0.686

Gnomad4 SAS AF: 0.489

Gnomad4 FIN AF: 0.632

Gnomad4 NFE AF: 0.628

Gnomad4 OTH AF: 0.585

Alfa AF: 0.623 Hom.: 65611

Bravo AF: 0.580

Asia WGS AF: 0.537 AC: 1868 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.99
DANN	Benign	0.35

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: rs391300; hg19: chr17-2216258;