rs7605146

Variant names:

• chr2-200319165-G-A
• rs7605146
• NM_001100423.2:c.-72-10266G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-200319165-G-A
• chr2-200319165-G-C
• chr2-200319165-G-T

Variant summary

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

The NM_001282744.2(SPATS2L):​c.18+10075G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 152,000 control chromosomes in the GnomAD database, including 11,365 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 0.36 (11365 hom., cov: 31)
• Consequence: SPATS2L NM_001282744.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.43
• Publications: 13 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001282744.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATS2L	NM_001100423.2	MANE Select	c.-72-10266G>A		intron	N/A	NP_001093893.1
	SPATS2L	NM_001282744.2		c.18+10075G>A		intron	N/A	NP_001269673.1
	SPATS2L	NM_001100422.1		c.-72-10266G>A		intron	N/A	NP_001093892.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATS2L	ENST00000409140.8	TSL:2 MANE Select	c.-72-10266G>A		intron	N/A	ENSP00000386730.3
	SPATS2L	ENST00000358677.9	TSL:1	c.-72-10266G>A		intron	N/A	ENSP00000351503.4
	SPATS2L	ENST00000360760.9	TSL:1	c.-72-10266G>A		intron	N/A	ENSP00000353989.5

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55182 AN: 151882 Hom.: 11361 Cov.: 31

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.363 AC: 55199 AN: 152000 Hom.: 11365 Cov.: 31 AF XY: 0.375 AC XY: 27868 AN XY: 74318

African (AFR) AF: 0.183 AC: 7591 AN: 41446

American (AMR) AF: 0.517 AC: 7907 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1315 AN: 3472

East Asian (EAS) AF: 0.723 AC: 3734 AN: 5166

South Asian (SAS) AF: 0.505 AC: 2432 AN: 4820

European-Finnish (FIN) AF: 0.450 AC: 4745 AN: 10544

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.386 AC: 26256 AN: 67958

Other (OTH) AF: 0.365 AC: 769 AN: 2104

Alfa AF: 0.305 Hom.: 1258

Bravo AF: 0.361

Asia WGS AF: 0.610 AC: 2115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.0050
DANN	Benign	0.55
PhyloP100		-2.4
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: rs7605146; hg19: chr2-201183888;