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

Variant summary

Our verdict is Benign. The variant received -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

Publications

11 publications found

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 was made for transcript

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 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

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

442

884

1325

1767

2209

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

334

668

1002

1336

1670

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.837

AC:

127391

AN:

152236

Hom.:

53474

Cov.:

AF XY:

0.834

AC XY:

62045

AN XY:

74434

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

1069

2137

3206

4274

5343

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

884

1768

2652

3536

4420

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

(source)

DANN

Benign

0.70

PhyloP100

-1.1

PromoterAI

0.043

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over