chr17-2319031-C-T

Variant names:

• chr17-2319031-C-T
• rs8081273
• NM_021947.3:c.399+102C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.184
• Publications: 16 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SRR	NM_021947.3	c.399+102C>T		intron_variant	Intron 4 of 7	ENST00000344595.10	NP_068766.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SRR	ENST00000344595.10	c.399+102C>T		intron_variant	Intron 4 of 7	1	NM_021947.3	ENSP00000339435.5

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69226 AN: 151696 Hom.: 16624 Cov.: 30

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

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

GnomAD4 genome AF: 0.457 AC: 69313 AN: 151814 Hom.: 16649 Cov.: 30 AF XY: 0.458 AC XY: 33968 AN XY: 74202

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

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.1
DANN	Benign	0.27
PhyloP100		-0.18
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: rs8081273; hg19: chr17-2222325; COSMIC: COSV56784232; COSMIC: COSV56784232;