chr3-113571621-T-C

Variant names:

• chr3-113571621-T-C
• rs13092825
• NM_017699.3:c.515+3911T>C

Variant summary

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

The NM_017699.3(SIDT1):​c.515+3911T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,158 control chromosomes in the GnomAD database, including 1,806 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 0.15 (1806 hom., cov: 33)
• Consequence: SIDT1 NM_017699.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 6 publications found

Genes affected

SIDT1 (HGNC:25967): (SID1 transmembrane family member 1) The protein encoded by this gene belongs to SID1 family of transmembrane dsRNA-gated channels. Family members transport dsRNA into cells and are required for systemic RNA interference. [provided by RefSeq, May 2017]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SIDT1	NM_017699.3	c.515+3911T>C		intron_variant	Intron 3 of 24	ENST00000264852.9	NP_060169.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SIDT1	ENST00000264852.9	c.515+3911T>C		intron_variant	Intron 3 of 24	2	NM_017699.3	ENSP00000264852.4
SIDT1	ENST00000393830.5	c.515+3911T>C		intron_variant	Intron 3 of 25	1		ENSP00000377416.4
SIDT1	ENST00000491730.5	n.982+3911T>C		intron_variant	Intron 3 of 5	5

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22907 AN: 152040 Hom.: 1803 Cov.: 33

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.0796

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.0985

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.151 AC: 22922 AN: 152158 Hom.: 1806 Cov.: 33 AF XY: 0.146 AC XY: 10894 AN XY: 74392

African (AFR) AF: 0.134 AC: 5543 AN: 41504

American (AMR) AF: 0.101 AC: 1544 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 575 AN: 3470

East Asian (EAS) AF: 0.0798 AC: 414 AN: 5188

South Asian (SAS) AF: 0.154 AC: 742 AN: 4822

European-Finnish (FIN) AF: 0.0985 AC: 1043 AN: 10594

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12591 AN: 67988

Other (OTH) AF: 0.130 AC: 274 AN: 2114

Alfa AF: 0.170 Hom.: 6440

Bravo AF: 0.149

Asia WGS AF: 0.0980 AC: 340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.45
PhyloP100		-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

Other links and lift over

dbSNP: rs13092825; hg19: chr3-113290468;