rs10484890

Variant names:

• chr6-10905813-C-T
• rs10484890
• NM_001040274.3:c.642-207C>T

Variant summary

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

The NM_001040274.3(SYCP2L):​c.642-207C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 152,128 control chromosomes in the GnomAD database, including 1,307 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 0.12 (1307 hom., cov: 32)
• Consequence: SYCP2L NM_001040274.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65
• Publications: 3 publications found

Genes affected

SYCP2L (HGNC:21537): (synaptonemal complex protein 2 like) Predicted to be involved in meiotic nuclear division. Predicted to act upstream of or within negative regulation of cell death. Located in condensed chromosome, centromeric region and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000272162 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SYCP2L	NM_001040274.3	c.642-207C>T		intron_variant	Intron 8 of 29	ENST00000283141.11	NP_001035364.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SYCP2L	ENST00000283141.11	c.642-207C>T		intron_variant	Intron 8 of 29	1	NM_001040274.3	ENSP00000283141.6
ENSG00000272162	ENST00000480294.1	n.*604-207C>T		intron_variant	Intron 10 of 18	2		ENSP00000417929.1
SYCP2L	ENST00000341041.8	n.642-207C>T		intron_variant	Intron 8 of 29	2		ENSP00000340320.4
SYCP2L	ENST00000487561.2	n.302+2850C>T		intron_variant	Intron 4 of 8	3		ENSP00000417870.1

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18522 AN: 152010 Hom.: 1307 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.0771

Gnomad AMR AF: 0.0833

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0381

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.122 AC: 18528 AN: 152128 Hom.: 1307 Cov.: 32 AF XY: 0.121 AC XY: 9010 AN XY: 74362

African (AFR) AF: 0.106 AC: 4383 AN: 41500

American (AMR) AF: 0.0832 AC: 1271 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 381 AN: 3472

East Asian (EAS) AF: 0.00232 AC: 12 AN: 5178

South Asian (SAS) AF: 0.0373 AC: 180 AN: 4822

European-Finnish (FIN) AF: 0.188 AC: 1983 AN: 10558

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 10002 AN: 67998

Other (OTH) AF: 0.106 AC: 224 AN: 2114

Alfa AF: 0.130 Hom.: 2482

Bravo AF: 0.114

Asia WGS AF: 0.0440 AC: 154 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	0.26
DANN	Benign	0.52
PhyloP100		-1.6
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: rs10484890; hg19: chr6-10906046;