rs2269399

Variant names:

• chr11-117195637-G-C
• rs2269399
• NM_001040455.2:c.2323-165G>C

Variant summary

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

The NM_001040455.2(SIDT2):​c.2323-165G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,196 control chromosomes in the GnomAD database, including 1,656 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 (1656 hom., cov: 32)
• Consequence: SIDT2 NM_001040455.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.386
• Publications: 8 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]

ENSG00000304501 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.255 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SIDT2	NM_001040455.2	MANE Select	c.2323-165G>C		intron	N/A	NP_001035545.1
	LOC100652768	NR_045215.1		n.1220C>G		non_coding_transcript_exon	Exon 8 of 8

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SIDT2	ENST00000324225.9	TSL:1 MANE Select	c.2323-165G>C		intron	N/A	ENSP00000314023.4
	SIDT2	ENST00000431081.6	TSL:1	c.2314-165G>C		intron	N/A	ENSP00000399635.2
	ENSG00000304501	ENST00000803863.1		n.816C>G		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18237 AN: 152078 Hom.: 1656 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0604

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.0903

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0755

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0615

Gnomad OTH AF: 0.100

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.120 AC: 18233 AN: 152196 Hom.: 1656 Cov.: 32 AF XY: 0.119 AC XY: 8846 AN XY: 74426

African (AFR) AF: 0.259 AC: 10738 AN: 41498

American (AMR) AF: 0.0602 AC: 921 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 393 AN: 3472

East Asian (EAS) AF: 0.0898 AC: 464 AN: 5168

South Asian (SAS) AF: 0.0999 AC: 482 AN: 4826

European-Finnish (FIN) AF: 0.0755 AC: 802 AN: 10616

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

European-Non Finnish (NFE) AF: 0.0615 AC: 4181 AN: 67990

Other (OTH) AF: 0.0988 AC: 209 AN: 2116

Alfa AF: 0.0960 Hom.: 135

Bravo AF: 0.127

Asia WGS AF: 0.0980 AC: 343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.2
DANN	Benign	0.55
PhyloP100		-0.39
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

Other links and lift over

dbSNP: rs2269399; hg19: chr11-117066353;