17-2312964-T-C

Variant names:

• chr17-2312964-T-C
• rs391300
• NM_021947.3:c.-4-2593T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 125 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SRR	NM_021947.3	c.-4-2593T>C		intron_variant	Intron 1 of 7	ENST00000344595.10	NP_068766.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SRR	ENST00000344595.10	c.-4-2593T>C		intron_variant	Intron 1 of 7	1	NM_021947.3	ENSP00000339435.5

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

African (AFR) AF: 0.480 AC: 19906 AN: 41440

American (AMR) AF: 0.612 AC: 9353 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.644 AC: 2237 AN: 3472

East Asian (EAS) AF: 0.686 AC: 3541 AN: 5162

South Asian (SAS) AF: 0.489 AC: 2359 AN: 4820

European-Finnish (FIN) AF: 0.632 AC: 6644 AN: 10510

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.628 AC: 42684 AN: 67996

Other (OTH) AF: 0.585 AC: 1234 AN: 2110

Alfa AF: 0.618 Hom.: 132715

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
PhyloP100		-0.37
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs391300; hg19: chr17-2216258;