6-10910386-C-G

Variant names:

• chr6-10910386-C-G
• rs9467921
• NM_001040274.3:c.872+186C>G

Variant summary

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

The NM_001040274.3(SYCP2L):​c.872+186C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 151,958 control chromosomes in the GnomAD database, including 8,753 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 0.32 (8753 hom., cov: 32)
• Consequence: SYCP2L NM_001040274.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.856
• Publications: 6 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SYCP2L	NM_001040274.3	c.872+186C>G		intron_variant	Intron 11 of 29	ENST00000283141.11	NP_001035364.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SYCP2L	ENST00000283141.11	c.872+186C>G		intron_variant	Intron 11 of 29	1	NM_001040274.3	ENSP00000283141.6
ENSG00000272162	ENST00000480294.1	n.*834+186C>G		intron_variant	Intron 13 of 18	2		ENSP00000417929.1
SYCP2L	ENST00000341041.8	n.872+186C>G		intron_variant	Intron 11 of 29	2		ENSP00000340320.4
SYCP2L	ENST00000487561.2	n.*25+186C>G		intron_variant	Intron 5 of 8	3		ENSP00000417870.1

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49206 AN: 151840 Hom.: 8737 Cov.: 32

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.324 AC: 49268 AN: 151958 Hom.: 8753 Cov.: 32 AF XY: 0.321 AC XY: 23845 AN XY: 74270

African (AFR) AF: 0.451 AC: 18695 AN: 41444

American (AMR) AF: 0.284 AC: 4342 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 1232 AN: 3466

East Asian (EAS) AF: 0.535 AC: 2763 AN: 5162

South Asian (SAS) AF: 0.310 AC: 1491 AN: 4814

European-Finnish (FIN) AF: 0.190 AC: 2005 AN: 10532

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17779 AN: 67950

Other (OTH) AF: 0.304 AC: 640 AN: 2108

Alfa AF: 0.138 Hom.: 219

Bravo AF: 0.338

Asia WGS AF: 0.395 AC: 1376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.050
DANN	Benign	0.34
PhyloP100		-0.86
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: rs9467921; hg19: chr6-10910619;