NM_005069.6:c.175+135G>A

Variant names:

• chr21-36700056-G-A
• rs2269188
• NM_005069.6:c.175+135G>A

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.175+135G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000263 in 761,566 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: 33)
  • Exomes 𝑓: 0.0000026 (0 hom.)
• Consequence: SIM2 NM_005069.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.318
• Publications: 7 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]

ENSG00000224269 (HGNC:):

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=-0.7).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SIM2	NM_005069.6	c.175+135G>A		intron_variant	Intron 1 of 10	ENST00000290399.11	NP_005060.1
SIM2	NM_009586.5	c.175+135G>A		intron_variant	Intron 1 of 9		NP_033664.2
SIM2	XM_017028442.3	c.175+135G>A		intron_variant	Intron 1 of 8		XP_016883931.1
SIM2	XM_047440953.1	c.175+135G>A		intron_variant	Intron 1 of 7		XP_047296909.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SIM2	ENST00000290399.11	c.175+135G>A		intron_variant	Intron 1 of 10	1	NM_005069.6	ENSP00000290399.6
SIM2	ENST00000460783.1	n.789+135G>A		intron_variant	Intron 1 of 1	1
ENSG00000224269	ENST00000430607.1	n.269-1213C>T		intron_variant	Intron 1 of 1	5
SIM2	ENST00000481185.1	n.788+135G>A		intron_variant	Intron 1 of 9	2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000263 AC: 2 AN: 761566 Hom.: 0 AF XY: 0.00000514 AC XY: 2 AN XY: 389390

African (AFR) AF: 0.00 AC: 0 AN: 14604

American (AMR) AF: 0.00 AC: 0 AN: 17326

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15384

East Asian (EAS) AF: 0.00 AC: 0 AN: 29452

South Asian (SAS) AF: 0.0000374 AC: 2 AN: 53530

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 36560

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2564

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 556534

Other (OTH) AF: 0.00 AC: 0 AN: 35612

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	4.2
DANN	Benign	0.91
PhyloP100		0.32

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: rs2269188; hg19: chr21-38072356;