Genetic Variant SSU72L5:p.Ser4Ser (chr11-4233299-C-T) – ACMG Classification: Benign (-7 pts)

Variant summary

Our verdict is Benign. The variant received -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_001414002.2(SSU72L5):c.12C>T(p.Ser4Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.000027 ( 0 hom., cov: 24)

Exomes 𝑓: 0.000038 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

SSU72L5
NM_001414002.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.635

Publications

0 publications found

Variant links:

Genes affected

SSU72L5 (HGNC:43624): (SSU72 like 5) Predicted to enable RNA polymerase II CTD heptapeptide repeat phosphatase activity. Predicted to be involved in dephosphorylation of RNA polymerase II C-terminal domain; mRNA polyadenylation; and termination of RNA polymerase II transcription. Predicted to be part of mRNA cleavage and polyadenylation specificity factor complex. [provided by Alliance of Genome Resources, Apr 2022]

SSU72L5 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -7 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

BP6

Variant 11-4233299-C-T is Benign according to our data. Variant chr11-4233299-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2641527.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.635 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001414002.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SSU72L5	NM_001414002.2	MANE Select	c.12C>T	p.Ser4Ser	synonymous	Exon 1 of 1	NP_001400931.1	A0A1W2PQ64

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SSU72L5	ENST00000639584.2	TSL:6 MANE Select	c.12C>T	p.Ser4Ser	synonymous	Exon 1 of 1	ENSP00000491949.1	A0A1W2PQ64

Frequencies

GnomAD3 genomes

AF:

0.0000269

AC:

AN:

148836

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000594

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000380

AC:

AN:

421052

Hom.:

Cov.:

AF XY:

0.0000407

AC XY:

AN XY:

221228

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

11584

American (AMR)

AF:

0.00

AC:

AN:

16354

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

12636

East Asian (EAS)

AF:

0.00

AC:

AN:

27918

South Asian (SAS)

AF:

0.00

AC:

AN:

35760

European-Finnish (FIN)

AF:

0.00

AC:

AN:

36930

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1818

European-Non Finnish (NFE)

AF:

0.0000591

AC:

AN:

253662

Other (OTH)

AF:

0.0000410

AC:

AN:

24390

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000269

AC:

AN:

148836

Hom.:

Cov.:

AF XY:

0.0000414

AC XY:

AN XY:

72380

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

40552

American (AMR)

AF:

0.00

AC:

AN:

14786

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3410

East Asian (EAS)

AF:

0.00

AC:

AN:

4928

South Asian (SAS)

AF:

0.00

AC:

AN:

4368

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10240

Middle Eastern (MID)

AF:

0.00

AC:

AN:

314

European-Non Finnish (NFE)

AF:

0.0000594

AC:

AN:

67298

Other (OTH)

AF:

0.00

AC:

AN:

2034

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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:

0.00

Hom.:

Bravo

AF:

0.0000302

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

1.4

(source)

DANN

Benign

0.50

PhyloP100

-0.64

PromoterAI

-0.012

Neutral

(source)

Splicing

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over