rs1012642

chr12-45959496-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCAF11	NM_004719.3	c.219+2204G>A		intron_variant		ENST00000369367.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCAF11	ENST00000369367.8	c.219+2204G>A		intron_variant		1	NM_004719.3	P1
SCAF11	ENST00000395454.6	c.219+2204G>A		intron_variant		1
SCAF11	ENST00000266589.10	c.267+2204G>A		intron_variant		5
SCAF11	ENST00000547018.5	c.14+2200G>A		intron_variant		5

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

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.509

Gnomad4 EAS AF: 0.524

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.403

Alfa AF: 0.467 Hom.: 20323

Bravo AF: 0.372

Asia WGS AF: 0.459 AC: 1595 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.3
Dann	Benign	0.71

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

LitVar

Other links and lift over

dbSNP: rs1012642; hg19: chr12-46353279;