rs11706066

chr3-113606309-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017699.3(SIDT1):c.1405-732T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 152,022 control chromosomes in the GnomAD database, including 7,291 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 0.29 (7291 hom., cov: 32)
  • Exomes 𝑓: 0.33 (0 hom.)
• Consequence: SIDT1 NM_017699.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SIDT1	NM_017699.3	c.1405-732T>C		intron_variant		ENST00000264852.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SIDT1	ENST00000264852.9	c.1405-732T>C		intron_variant		2	NM_017699.3	P4
SIDT1	ENST00000393830.4	c.1405-732T>C		intron_variant		1		A2
SIDT1	ENST00000463226.1	n.314+1333T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44350 AN: 151898 Hom.: 7281 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.269

GnomAD4 exome AF: 0.333 AC: 2 AN: 6 Hom.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

Gnomad4 ASJ exome AF: 0.500

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.292 AC: 44385 AN: 152016 Hom.: 7291 Cov.: 32 AF XY: 0.294 AC XY: 21855 AN XY: 74266

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.313

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.369

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.394

Gnomad4 NFE AF: 0.349

Gnomad4 OTH AF: 0.274

Alfa AF: 0.322 Hom.: 2345

Bravo AF: 0.281

Asia WGS AF: 0.412 AC: 1429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	4.7
Dann	Benign	0.51

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: rs11706066; hg19: chr3-113325156;