rs2306472

Variant names:

• chr11-117187346-C-T
• rs2306472
• NM_001040455.2:c.1016-32C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001040455.2(SIDT2):​c.1016-32C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0727 in 1,602,008 control chromosomes in the GnomAD database, including 5,904 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 0.12 (1636 hom., cov: 31)
  • Exomes 𝑓: 0.068 (4268 hom.)
• Consequence: SIDT2 NM_001040455.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.505
• Publications: 7 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SIDT2	NM_001040455.2	MANE Select	c.1016-32C>T		intron	N/A	NP_001035545.1	Q8NBJ9-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SIDT2	ENST00000324225.9	TSL:1 MANE Select	c.1016-32C>T		intron	N/A	ENSP00000314023.4	Q8NBJ9-1
	SIDT2	ENST00000431081.6	TSL:1	c.1028-32C>T		intron	N/A	ENSP00000399635.2	F5H8L4
	SIDT2	ENST00000278951.11	TSL:5	c.1016-32C>T		intron	N/A	ENSP00000278951.7	C9JBG5

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17931 AN: 151928 Hom.: 1636 Cov.: 31

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.00879

Gnomad AMR AF: 0.0581

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.0899

Gnomad SAS AF: 0.0993

Gnomad FIN AF: 0.0753

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0589

Gnomad OTH AF: 0.0977

GnomAD2 exomes AF: 0.0821 AC: 20645 AN: 251406 AF XY: 0.0798

Gnomad AFR exome AF: 0.263

Gnomad AMR exome AF: 0.0497

Gnomad ASJ exome AF: 0.0986

Gnomad EAS exome AF: 0.102

Gnomad FIN exome AF: 0.0769

Gnomad NFE exome AF: 0.0591

Gnomad OTH exome AF: 0.0701

GnomAD4 exome AF: 0.0680 AC: 98555 AN: 1449962 Hom.: 4268 Cov.: 29 AF XY: 0.0682 AC XY: 49239 AN XY: 722032

African (AFR) AF: 0.263 AC: 8755 AN: 33228

American (AMR) AF: 0.0525 AC: 2345 AN: 44700

Ashkenazi Jewish (ASJ) AF: 0.0985 AC: 2569 AN: 26070

East Asian (EAS) AF: 0.103 AC: 4080 AN: 39642

South Asian (SAS) AF: 0.0929 AC: 7988 AN: 86028

European-Finnish (FIN) AF: 0.0750 AC: 4006 AN: 53418

Middle Eastern (MID) AF: 0.117 AC: 669 AN: 5738

European-Non Finnish (NFE) AF: 0.0576 AC: 63442 AN: 1101138

Other (OTH) AF: 0.0784 AC: 4701 AN: 60000

GnomAD4 genome AF: 0.118 AC: 17927 AN: 152046 Hom.: 1636 Cov.: 31 AF XY: 0.117 AC XY: 8689 AN XY: 74326

African (AFR) AF: 0.258 AC: 10690 AN: 41408

American (AMR) AF: 0.0579 AC: 885 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 367 AN: 3466

East Asian (EAS) AF: 0.0893 AC: 462 AN: 5172

South Asian (SAS) AF: 0.0985 AC: 475 AN: 4822

European-Finnish (FIN) AF: 0.0753 AC: 797 AN: 10590

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0589 AC: 4005 AN: 67990

Other (OTH) AF: 0.0962 AC: 203 AN: 2110

Alfa AF: 0.0954 Hom.: 249

Bravo AF: 0.125

Asia WGS AF: 0.0960 AC: 339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.2
DANN	Benign	0.56
PhyloP100		-0.51
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2306472;

hg19: chr11-117058062;

COSMIC: COSV54057255;

COSMIC: COSV54057255;