NM_001040455.2:c.1736-224T>A

Variant names:

• chr11-117191654-T-A
• rs1242229
• NM_001040455.2:c.1736-224T>A

Variant summary

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

The NM_001040455.2(SIDT2):​c.1736-224T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SIDT2 NM_001040455.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440
• Publications: 9 publications found

Genes affected

SIDT2 (HGNC:24272): (SID1 transmembrane family member 2) Predicted to enable several functions, including AP-1 adaptor complex binding activity; AP-2 adaptor complex binding activity; and RNA transmembrane transporter activity. Involved in RNA transport. Located in lysosomal membrane and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.83).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001040455.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SIDT2	NM_001040455.2	MANE Select	c.1736-224T>A		intron	N/A	NP_001035545.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SIDT2	ENST00000324225.9	TSL:1 MANE Select	c.1736-224T>A		intron	N/A	ENSP00000314023.4
	SIDT2	ENST00000431081.6	TSL:1	c.1727-224T>A		intron	N/A	ENSP00000399635.2
	SIDT2	ENST00000525065.1	TSL:2	n.927T>A		non_coding_transcript_exon	Exon 1 of 3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 449902 Hom.: 0 Cov.: 5 AF XY: 0.00 AC XY: 0 AN XY: 237134

African (AFR) AF: 0.00 AC: 0 AN: 12436

American (AMR) AF: 0.00 AC: 0 AN: 17452

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13356

East Asian (EAS) AF: 0.00 AC: 0 AN: 29852

South Asian (SAS) AF: 0.00 AC: 0 AN: 45184

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 29756

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1994

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 274190

Other (OTH) AF: 0.00 AC: 0 AN: 25682

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 32968

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.8
DANN	Benign	0.81
PhyloP100		-0.044

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: rs1242229; hg19: chr11-117062370;