2-200389448-A-G

Variant names:

• chr2-200389448-A-G
• rs4674015
• ENST00000459656.5:n.481A>G

Variant summary

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

The NM_001100423.2(SPATS2L):​c.39+165A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.683 in 533,408 control chromosomes in the GnomAD database, including 126,559 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 0.65 (32773 hom., cov: 33)
  • Exomes 𝑓: 0.70 (93786 hom.)
• Consequence: SPATS2L NM_001100423.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.480
• Publications: 5 publications found

Genes affected

SPATS2L (HGNC:24574): (spermatogenesis associated serine rich 2 like) Enables RNA binding activity. Located in cytosol; nucleolus; and nucleoplasm. Part of protein-containing complex. [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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPATS2L	NM_001100423.2	c.39+165A>G		intron_variant	Intron 3 of 12	ENST00000409140.8	NP_001093893.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPATS2L	ENST00000409140.8	c.39+165A>G		intron_variant	Intron 3 of 12	2	NM_001100423.2	ENSP00000386730.3

Frequencies

GnomAD3 genomes AF: 0.645 AC: 98121 AN: 152036 Hom.: 32747 Cov.: 33

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.811

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.650

GnomAD4 exome AF: 0.698 AC: 266265 AN: 381254 Hom.: 93786 Cov.: 4 AF XY: 0.703 AC XY: 140637 AN XY: 200036

African (AFR) AF: 0.477 AC: 5203 AN: 10902

American (AMR) AF: 0.761 AC: 9897 AN: 13012

Ashkenazi Jewish (ASJ) AF: 0.736 AC: 8863 AN: 12038

East Asian (EAS) AF: 0.660 AC: 18568 AN: 28122

South Asian (SAS) AF: 0.794 AC: 23290 AN: 29342

European-Finnish (FIN) AF: 0.696 AC: 21272 AN: 30564

Middle Eastern (MID) AF: 0.702 AC: 2342 AN: 3338

European-Non Finnish (NFE) AF: 0.697 AC: 161406 AN: 231412

Other (OTH) AF: 0.685 AC: 15424 AN: 22524

GnomAD4 genome AF: 0.645 AC: 98200 AN: 152154 Hom.: 32773 Cov.: 33 AF XY: 0.656 AC XY: 48774 AN XY: 74382

African (AFR) AF: 0.464 AC: 19256 AN: 41496

American (AMR) AF: 0.741 AC: 11330 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.733 AC: 2544 AN: 3472

East Asian (EAS) AF: 0.675 AC: 3493 AN: 5176

South Asian (SAS) AF: 0.811 AC: 3914 AN: 4828

European-Finnish (FIN) AF: 0.722 AC: 7645 AN: 10586

Middle Eastern (MID) AF: 0.675 AC: 197 AN: 292

European-Non Finnish (NFE) AF: 0.704 AC: 47852 AN: 67988

Other (OTH) AF: 0.650 AC: 1375 AN: 2114

Alfa AF: 0.684 Hom.: 51740

Bravo AF: 0.636

Asia WGS AF: 0.720 AC: 2505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.14
DANN	Benign	0.38
PhyloP100		-0.48
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: rs4674015; hg19: chr2-201254171; COSMIC: COSV62353686; COSMIC: COSV62353686;