rs1012642

Variant names:

• chr12-45959496-C-T
• rs1012642
• NM_004719.3:c.219+2204G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004719.3(SCAF11):​c.219+2204G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 152,034 control chromosomes in the GnomAD database, including 13,419 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 0.39 (13419 hom., cov: 32)
• Consequence: SCAF11 NM_004719.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.329
• Publications: 4 publications found

Genes affected

SCAF11 (HGNC:10784): (SR-related CTD associated factor 11) Enables RNA binding activity. Involved in spliceosomal complex assembly. Located in nuclear body and nucleolus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004719.3. 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
	SCAF11	NM_004719.3	MANE Select	c.219+2204G>A		intron	N/A	NP_004710.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCAF11	ENST00000369367.8	TSL:1 MANE Select	c.219+2204G>A		intron	N/A	ENSP00000358374.3
	SCAF11	ENST00000395454.6	TSL:1	c.219+2204G>A		intron	N/A	ENSP00000378840.2
	SCAF11	ENST00000943613.1		c.219+2204G>A		intron	N/A	ENSP00000613672.1

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59447 AN: 151916 Hom.: 13403 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.398

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.391 AC: 59473 AN: 152034 Hom.: 13419 Cov.: 32 AF XY: 0.395 AC XY: 29364 AN XY: 74312

African (AFR) AF: 0.152 AC: 6304 AN: 41470

American (AMR) AF: 0.394 AC: 6020 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.509 AC: 1765 AN: 3468

East Asian (EAS) AF: 0.524 AC: 2707 AN: 5162

South Asian (SAS) AF: 0.515 AC: 2485 AN: 4822

European-Finnish (FIN) AF: 0.523 AC: 5513 AN: 10550

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.488 AC: 33204 AN: 67972

Other (OTH) AF: 0.403 AC: 851 AN: 2110

Alfa AF: 0.465 Hom.: 24068

Bravo AF: 0.372

Asia WGS AF: 0.459 AC: 1595 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.71
PhyloP100		-0.33
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1012642; hg19: chr12-46353279;