rs2306472

Positions:

• chr11-117187346-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SIDT2	NM_001040455.2	c.1016-32C>T		intron_variant		ENST00000324225.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SIDT2	ENST00000324225.9	c.1016-32C>T		intron_variant		1	NM_001040455.2	P3

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

GnomAD3 exomes AF: 0.0821 AC: 20645 AN: 251406 Hom.: 1254 AF XY: 0.0798 AC XY: 10845 AN XY: 135878

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 SAS exome AF: 0.0970

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

Gnomad4 AFR exome AF: 0.263

Gnomad4 AMR exome AF: 0.0525

Gnomad4 ASJ exome AF: 0.0985

Gnomad4 EAS exome AF: 0.103

Gnomad4 SAS exome AF: 0.0929

Gnomad4 FIN exome AF: 0.0750

Gnomad4 NFE exome AF: 0.0576

Gnomad4 OTH exome AF: 0.0784

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

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.0579

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.0893

Gnomad4 SAS AF: 0.0985

Gnomad4 FIN AF: 0.0753

Gnomad4 NFE AF: 0.0589

Gnomad4 OTH AF: 0.0962

Alfa AF: 0.0919 Hom.: 225

Bravo AF: 0.125

Asia WGS AF: 0.0960 AC: 339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.2
DANN	Benign	0.56
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs2306472; hg19: chr11-117058062; COSMIC: COSV54057255; COSMIC: COSV54057255;