chr6-10886716-C-T

Variant names:

• chr6-10886716-C-T
• rs9379896
• ENST00000480294.1:n.101-4797C>T

Variant summary

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

The ENST00000480294.1(ENSG00000272162):​n.101-4797C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.829 in 214,190 control chromosomes in the GnomAD database, including 73,974 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 0.84 (53474 hom., cov: 34)
  • Exomes 𝑓: 0.81 (20500 hom.)
• Consequence: ENSG00000272162 ENST00000480294.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 11 publications found

Genes affected

ENSG00000272162 (HGNC:):

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000272162	ENST00000480294.1	n.101-4797C>T		intron_variant	Intron 3 of 18	2		ENSP00000417929.1
SYCP2L	ENST00000341041.8	n.-411C>T		upstream_gene_variant		2		ENSP00000340320.4

Frequencies

GnomAD3 genomes AF: 0.837 AC: 127286 AN: 152118 Hom.: 53429 Cov.: 34

Gnomad AFR AF: 0.885

Gnomad AMI AF: 0.970

Gnomad AMR AF: 0.856

Gnomad ASJ AF: 0.843

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.804

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.822

Gnomad OTH AF: 0.837

GnomAD4 exome AF: 0.809 AC: 50138 AN: 61954 Hom.: 20500 AF XY: 0.807 AC XY: 26336 AN XY: 32622

African (AFR) AF: 0.887 AC: 2979 AN: 3360

American (AMR) AF: 0.855 AC: 4530 AN: 5300

Ashkenazi Jewish (ASJ) AF: 0.824 AC: 1347 AN: 1634

East Asian (EAS) AF: 0.662 AC: 3424 AN: 5172

South Asian (SAS) AF: 0.789 AC: 5760 AN: 7296

European-Finnish (FIN) AF: 0.795 AC: 1682 AN: 2116

Middle Eastern (MID) AF: 0.841 AC: 185 AN: 220

European-Non Finnish (NFE) AF: 0.820 AC: 27716 AN: 33802

Other (OTH) AF: 0.824 AC: 2515 AN: 3054

GnomAD4 genome AF: 0.837 AC: 127391 AN: 152236 Hom.: 53474 Cov.: 34 AF XY: 0.834 AC XY: 62045 AN XY: 74434

African (AFR) AF: 0.885 AC: 36773 AN: 41536

American (AMR) AF: 0.856 AC: 13090 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.843 AC: 2924 AN: 3468

East Asian (EAS) AF: 0.655 AC: 3382 AN: 5166

South Asian (SAS) AF: 0.804 AC: 3880 AN: 4828

European-Finnish (FIN) AF: 0.804 AC: 8525 AN: 10604

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.822 AC: 55907 AN: 68018

Other (OTH) AF: 0.837 AC: 1769 AN: 2114

Alfa AF: 0.823 Hom.: 114355

Bravo AF: 0.843

Asia WGS AF: 0.778 AC: 2706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.0
DANN	Benign	0.70
PhyloP100		-1.1
PromoterAI		0.043	Neutral
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: rs9379896; hg19: chr6-10886949;