Genetic Variant NM_001136234.3:c.1514C>T (chrX-24364274-C-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001136234.3(SUPT20HL1):c.1514C>T(p.Ala505Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000109 in 918,523 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 5/5 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0000095 ( 0 hom., 0 hem., cov: 22)

Exomes 𝑓: 0.000011 ( 0 hom. 3 hem. )

Consequence

SUPT20HL1
NM_001136234.3 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.793

Publications

0 publications found

Variant links:

Genes affected

SUPT20HL1 (HGNC:30773): (SUPT20H like 1) Predicted to enable transcription coregulator activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be part of SAGA complex. [provided by Alliance of Genome Resources, Apr 2022]

SUPT20HL1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant X-24364274-C-T is Benign according to our data. Variant chrX-24364274-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 3777860.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Hemizygotes in GnomAdExome4 at 3 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001136234.3. 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
	SUPT20HL1	NM_001136234.3	MANE Select	c.1514C>T	p.Ala505Val	missense	Exon 1 of 1	NP_001129706.3	A0A7I2YQ69

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SUPT20HL1	ENST00000686983.1	MANE Select	c.1514C>T	p.Ala505Val	missense	Exon 1 of 1	ENSP00000509731.1	A0A7I2YQ69
	SUPT20HL1	ENST00000436466.2	TSL:6	c.1514C>T	p.Ala505Val	missense	Exon 2 of 2	ENSP00000502907.1	A0A7I2YQ69

Frequencies

GnomAD3 genomes

AF:

0.00000954

AC:

AN:

104860

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:

0.0000195

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.0000111

AC:

AN:

813663

Hom.:

Cov.:

AF XY:

0.0000126

AC XY:

AN XY:

238941

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

17960

American (AMR)

AF:

0.00

AC:

AN:

27128

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

16533

East Asian (EAS)

AF:

0.00

AC:

AN:

25643

South Asian (SAS)

AF:

0.00

AC:

AN:

44166

European-Finnish (FIN)

AF:

0.00

AC:

AN:

36228

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3534

European-Non Finnish (NFE)

AF:

0.0000132

AC:

AN:

606532

Other (OTH)

AF:

0.0000278

AC:

AN:

35939

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.592

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

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

AF:

0.00000954

AC:

AN:

104860

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

28930

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

27655

American (AMR)

AF:

0.00

AC:

AN:

9743

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2489

East Asian (EAS)

AF:

0.00

AC:

AN:

3409

South Asian (SAS)

AF:

0.00

AC:

AN:

2341

European-Finnish (FIN)

AF:

0.00

AC:

AN:

5552

Middle Eastern (MID)

AF:

0.00

AC:

AN:

234

European-Non Finnish (NFE)

AF:

0.0000195

AC:

AN:

51368

Other (OTH)

AF:

0.00

AC:

AN:

1395

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00

Hom.:

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

AlphaMissense

Benign

0.25

BayesDel_noAF

Benign

-0.89

CADD

Benign

4.0

(source)

DANN

Benign

0.45

PhyloP100

-0.79

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over