11-117191654-T-C

Variant names:

• chr11-117191654-T-C
• rs1242229
• NM_001040455.2:c.1736-224T>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.1736-224T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.844 in 601,726 control chromosomes in the GnomAD database, including 218,050 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 0.86 (57479 hom., cov: 33)
  • Exomes 𝑓: 0.84 (160571 hom.)
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SIDT2	NM_001040455.2	c.1736-224T>C		intron_variant	Intron 18 of 25	ENST00000324225.9	NP_001035545.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SIDT2	ENST00000324225.9	c.1736-224T>C		intron_variant	Intron 18 of 25	1	NM_001040455.2	ENSP00000314023.4

Frequencies

GnomAD3 genomes AF: 0.864 AC: 131490 AN: 152160 Hom.: 57438 Cov.: 33

Gnomad AFR AF: 0.907

Gnomad AMI AF: 0.988

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.857

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.858

Gnomad MID AF: 0.838

Gnomad NFE AF: 0.893

Gnomad OTH AF: 0.863

GnomAD4 exome AF: 0.837 AC: 376305 AN: 449448 Hom.: 160571 Cov.: 5 AF XY: 0.828 AC XY: 196051 AN XY: 236880

African (AFR) AF: 0.907 AC: 11266 AN: 12422

American (AMR) AF: 0.810 AC: 14115 AN: 17416

Ashkenazi Jewish (ASJ) AF: 0.853 AC: 11381 AN: 13344

East Asian (EAS) AF: 0.533 AC: 15879 AN: 29784

South Asian (SAS) AF: 0.654 AC: 29531 AN: 45134

European-Finnish (FIN) AF: 0.863 AC: 25679 AN: 29744

Middle Eastern (MID) AF: 0.815 AC: 1626 AN: 1994

European-Non Finnish (NFE) AF: 0.895 AC: 245167 AN: 273954

Other (OTH) AF: 0.844 AC: 21661 AN: 25656

GnomAD4 genome AF: 0.864 AC: 131576 AN: 152278 Hom.: 57479 Cov.: 33 AF XY: 0.856 AC XY: 63740 AN XY: 74456

African (AFR) AF: 0.907 AC: 37695 AN: 41562

American (AMR) AF: 0.811 AC: 12408 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.857 AC: 2975 AN: 3470

East Asian (EAS) AF: 0.507 AC: 2625 AN: 5176

South Asian (SAS) AF: 0.643 AC: 3094 AN: 4814

European-Finnish (FIN) AF: 0.858 AC: 9107 AN: 10612

Middle Eastern (MID) AF: 0.839 AC: 245 AN: 292

European-Non Finnish (NFE) AF: 0.893 AC: 60718 AN: 68024

Other (OTH) AF: 0.855 AC: 1808 AN: 2114

Alfa AF: 0.878 Hom.: 32968

Bravo AF: 0.866

Asia WGS AF: 0.608 AC: 2117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.2
DANN	Benign	0.84
PhyloP100		-0.044
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: rs1242229; hg19: chr11-117062370; COSMIC: COSV54057688; COSMIC: COSV54057688;