rs2153157

Variant names:

• chr6-10897255-G-A
• rs2153157
• NM_001040274.3:c.337-756G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-10897255-G-A
• chr6-10897255-G-C
• chr6-10897255-G-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.337-756G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 151,980 control chromosomes in the GnomAD database, including 23,862 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 0.55 (23862 hom., cov: 32)
• Consequence: SYCP2L NM_001040274.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26
• Publications: 50 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SYCP2L	NM_001040274.3	c.337-756G>A		intron_variant	Intron 4 of 29	ENST00000283141.11	NP_001035364.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SYCP2L	ENST00000283141.11	c.337-756G>A		intron_variant	Intron 4 of 29	1	NM_001040274.3	ENSP00000283141.6
ENSG00000272162	ENST00000480294.1	n.*299-756G>A		intron_variant	Intron 6 of 18	2		ENSP00000417929.1
SYCP2L	ENST00000341041.8	n.337-756G>A		intron_variant	Intron 4 of 29	2		ENSP00000340320.4

Frequencies

GnomAD3 genomes AF: 0.546 AC: 82896 AN: 151862 Hom.: 23831 Cov.: 32

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.546 AC: 82969 AN: 151980 Hom.: 23862 Cov.: 32 AF XY: 0.542 AC XY: 40239 AN XY: 74268

African (AFR) AF: 0.722 AC: 29912 AN: 41434

American (AMR) AF: 0.439 AC: 6709 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1525 AN: 3470

East Asian (EAS) AF: 0.672 AC: 3473 AN: 5168

South Asian (SAS) AF: 0.448 AC: 2160 AN: 4824

European-Finnish (FIN) AF: 0.423 AC: 4459 AN: 10536

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.484 AC: 32913 AN: 67962

Other (OTH) AF: 0.539 AC: 1138 AN: 2110

Alfa AF: 0.507 Hom.: 89048

Bravo AF: 0.559

Asia WGS AF: 0.528 AC: 1837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.35
DANN	Benign	0.68
PhyloP100		-2.3
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: rs2153157; hg19: chr6-10897488; COSMIC: COSV51658250; COSMIC: COSV51658250;