dbSNP rs12104272: SCAF1:c.-6-226G>A (chr19-49644795-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_021228.3(SCAF1):c.-6-226G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 387,320 control chromosomes in the GnomAD database, including 29,966 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 0.44 ( 16885 hom., cov: 31)

Exomes 𝑓: 0.32 ( 13081 hom. )

Consequence

SCAF1
NM_021228.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.131

Publications

24 publications found

Variant links:

Genes affected

SCAF1 (HGNC:30403): (SR-related CTD associated factor 1) Enables RNA polymerase II C-terminal domain binding activity. Predicted to be involved in RNA splicing; mRNA processing; and transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

SCAF1 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=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
SCAF1	NM_021228.3 link	c.-6-226G>A	intron_variant	Intron 1 of 10	ENST00000360565.8	NP_067051.2
SCAF1	XM_011527194.4 link	c.4-226G>A	intron_variant	Intron 1 of 10		XP_011525496.1
SCAF1	XM_005259122.6 link	c.-6-226G>A	intron_variant	Intron 1 of 10		XP_005259179.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
SCAF1	ENST00000360565.8 link	c.-6-226G>A	intron_variant	Intron 1 of 10	2	NM_021228.3	ENSP00000353769.2
SCAF1	ENST00000598359.5 link	c.-6-226G>A	intron_variant	Intron 1 of 6	3		ENSP00000473210.1
SCAF1	ENST00000595242.3 link	c.-232G>A	upstream_gene_variant		3		ENSP00000472276.1
SCAF1	ENST00000601038.5 link	c.-232G>A	upstream_gene_variant		3		ENSP00000472649.1

Frequencies

GnomAD3 genomes

AF:

0.435

AC:

65999

AN:

151830

Hom.:

16841

Cov.:

show subpopulations

Gnomad AFR

AF:

0.727

Gnomad AMI

AF:

0.420

Gnomad AMR

AF:

0.378

Gnomad ASJ

AF:

0.331

Gnomad EAS

AF:

0.273

Gnomad SAS

AF:

0.334

Gnomad FIN

AF:

0.252

Gnomad MID

AF:

0.440

Gnomad NFE

AF:

0.324

Gnomad OTH

AF:

0.413

GnomAD4 exome

AF:

0.318

AC:

74779

AN:

235372

Hom.:

13081

Cov.:

AF XY:

0.316

AC XY:

38495

AN XY:

121702

show subpopulations

African (AFR)

AF:

0.718

AC:

4337

AN:

6042

American (AMR)

AF:

0.348

AC:

2439

AN:

7004

Ashkenazi Jewish (ASJ)

AF:

0.318

AC:

2654

AN:

8358

East Asian (EAS)

AF:

0.253

AC:

4512

AN:

17840

South Asian (SAS)

AF:

0.305

AC:

4402

AN:

14410

European-Finnish (FIN)

AF:

0.250

AC:

4261

AN:

17070

Middle Eastern (MID)

AF:

0.413

AC:

475

AN:

1150

European-Non Finnish (NFE)

AF:

0.312

AC:

46416

AN:

148580

Other (OTH)

AF:

0.354

AC:

5283

AN:

14918

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

2322

4644

6965

9287

11609

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

230

460

690

920

1150

<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:

0.435

AC:

66098

AN:

151948

Hom.:

16885

Cov.:

AF XY:

0.426

AC XY:

31651

AN XY:

74284

show subpopulations

African (AFR)

AF:

0.727

AC:

30119

AN:

41430

American (AMR)

AF:

0.378

AC:

5771

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.331

AC:

1147

AN:

3464

East Asian (EAS)

AF:

0.274

AC:

1417

AN:

5180

South Asian (SAS)

AF:

0.332

AC:

1597

AN:

4806

European-Finnish (FIN)

AF:

0.252

AC:

2662

AN:

10556

Middle Eastern (MID)

AF:

0.435

AC:

128

AN:

294

European-Non Finnish (NFE)

AF:

0.324

AC:

21997

AN:

67936

Other (OTH)

AF:

0.417

AC:

879

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1709

3418

5126

6835

8544

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

570

1140

1710

2280

2850

<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:

0.361

Hom.:

13113

Bravo

AF:

0.458

Asia WGS

AF:

0.398

AC:

1380

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.47

(source)

DANN

Benign

0.61

PhyloP100

-0.13

PromoterAI

0.0080

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