Genetic Variant ENSG00000272162:n.101-4797C>T (chr6-10886716-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.08

Variant links:

Genes affected

ENSG00000272162 (HGNC:):

ENSG00000272162 links:

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]

SYCP2L links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 link	n.101-4797C>T		intron_variant	Intron 3 of 18	2		ENSP00000417929.1		F8WBI7
SYCP2L	ENST00000341041.8 link	n.-411C>T		upstream_gene_variant		2		ENSP00000340320.4		Q5T4T6-2

Frequencies

GnomAD3 genomes

AF:

0.837

AC:

127286

AN:

152118

Hom.:

53429

Cov.:

show subpopulations

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

show subpopulations

Gnomad4 AFR exome

AF:

0.887

Gnomad4 AMR exome

AF:

0.855

Gnomad4 ASJ exome

AF:

0.824

Gnomad4 EAS exome

AF:

0.662

Gnomad4 SAS exome

AF:

0.789

Gnomad4 FIN exome

AF:

0.795

Gnomad4 NFE exome

AF:

0.820

Gnomad4 OTH exome

AF:

0.824

GnomAD4 genome

AF:

0.837

AC:

127391

AN:

152236

Hom.:

53474

Cov.:

AF XY:

0.834

AC XY:

62045

AN XY:

74434

show subpopulations

Gnomad4 AFR

AF:

0.885

Gnomad4 AMR

AF:

0.856

Gnomad4 ASJ

AF:

0.843

Gnomad4 EAS

AF:

0.655

Gnomad4 SAS

AF:

0.804

Gnomad4 FIN

AF:

0.804

Gnomad4 NFE

AF:

0.822

Gnomad4 OTH

AF:

0.837

Alfa

AF:

0.823

Hom.:

33515

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

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over