21-31706612-G-A

Position:

• chr21-31706612-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020706.2(SCAF4):​c.31-255C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 449,318 control chromosomes in the GnomAD database, including 12,788 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 0.26 (7365 hom., cov: 32)
  • Exomes 𝑓: 0.16 (5423 hom.)
• Consequence: SCAF4 NM_020706.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58

Genes affected

SCAF4 (HGNC:19304): (SR-related CTD associated factor 4) This gene likely encodes a member of the arginine/serine-rich splicing factor family. A similar protein in Rat appears to bind the large subunit of RNA polymerase II and provide a link between transcription and pre-mRNA splicing. Alternatively spliced transcript variants have been described. [provided by RefSeq, Feb 2009]

HMGN1P2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.504 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SCAF4	NM_020706.2	c.31-255C>T		intron_variant		ENST00000286835.12	NP_065757.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SCAF4	ENST00000286835.12	c.31-255C>T		intron_variant		1	NM_020706.2	ENSP00000286835.7

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39225 AN: 151876 Hom.: 7348 Cov.: 32

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.236

GnomAD4 exome AF: 0.162 AC: 48071 AN: 297324 Hom.: 5423 Cov.: 0 AF XY: 0.158 AC XY: 24601 AN XY: 155318

Gnomad4 AFR exome AF: 0.517

Gnomad4 AMR exome AF: 0.303

Gnomad4 ASJ exome AF: 0.100

Gnomad4 EAS exome AF: 0.378

Gnomad4 SAS exome AF: 0.154

Gnomad4 FIN exome AF: 0.163

Gnomad4 NFE exome AF: 0.118

Gnomad4 OTH exome AF: 0.185

GnomAD4 genome AF: 0.258 AC: 39288 AN: 151994 Hom.: 7365 Cov.: 32 AF XY: 0.259 AC XY: 19216 AN XY: 74292

Gnomad4 AFR AF: 0.510

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.426

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.238

Alfa AF: 0.136 Hom.: 2376

Bravo AF: 0.281

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.46
DANN	Benign	0.72

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: rs2833485; hg19: chr21-33078925;