rs2269399

chr11-117195637-G-C

Variant summary

Our verdict is Benign. Variant got -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

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]

LOC100652768 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SIDT2	NM_001040455.2	c.2323-165G>C		intron_variant		ENST00000324225.9
LOC100652768	NR_045215.1	n.1220C>G		non_coding_transcript_exon_variant	8/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SIDT2	ENST00000324225.9	c.2323-165G>C		intron_variant		1	NM_001040455.2	P3

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

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.0602

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.0898

Gnomad4 SAS AF: 0.0999

Gnomad4 FIN AF: 0.0755

Gnomad4 NFE AF: 0.0615

Gnomad4 OTH AF: 0.0988

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	2.2
Dann	Benign	0.55

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

Publications

LitVar

Other links and lift over

dbSNP: rs2269399; hg19: chr11-117066353;