NM_005069.6:c.457+29C>T

Variant names:

• chr21-36719958-C-T
• rs78455239
• NM_005069.6:c.457+29C>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_005069.6(SIM2):​c.457+29C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000867 in 1,152,898 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 8.7e-7 (0 hom.)
• Consequence: SIM2 NM_005069.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.584
• Publications: 0 publications found

Genes affected

SIM2 (HGNC:10883): (SIM bHLH transcription factor 2) This gene represents a homolog of the Drosophila single-minded (sim) gene, which encodes a transcription factor that is a master regulator of neurogenesis. The encoded protein is ubiquitinated by RING-IBR-RING-type E3 ubiquitin ligases, including the parkin RBR E3 ubiquitin protein ligase. This gene maps within the so-called Down syndrome chromosomal region, and is thus thought to contribute to some specific Down syndrome phenotypes. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Sep 2014]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005069.6. 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
	SIM2	NM_005069.6	MANE Select	c.457+29C>T		intron	N/A	NP_005060.1	Q14190-1
	SIM2	NM_009586.5		c.457+29C>T		intron	N/A	NP_033664.2	Q14190-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SIM2	ENST00000290399.11	TSL:1 MANE Select	c.457+29C>T		intron	N/A	ENSP00000290399.6	Q14190-1
	SIM2	ENST00000431229.1	TSL:1	c.268+29C>T		intron	N/A	ENSP00000392003.1	H7BZX8
	SIM2	ENST00000483178.2	TSL:3	c.195C>T	p.Asn65Asn	synonymous	Exon 2 of 2	ENSP00000476273.1	V9GY04

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 8.67e-7 AC: 1 AN: 1152898 Hom.: 0 Cov.: 18 AF XY: 0.00000170 AC XY: 1 AN XY: 587416

African (AFR) AF: 0.00 AC: 0 AN: 26318

American (AMR) AF: 0.0000235 AC: 1 AN: 42526

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 23994

East Asian (EAS) AF: 0.00 AC: 0 AN: 38414

South Asian (SAS) AF: 0.00 AC: 0 AN: 79570

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 46694

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5112

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 840192

Other (OTH) AF: 0.00 AC: 0 AN: 50078

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.9
DANN	Benign	0.71
PhyloP100		0.58

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs78455239; hg19: chr21-38092259;