rs6769767

Positions:

• chr3-113563479-A-G

Variant summary

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

The NM_017699.3(SIDT1):​c.223-2941A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 152,146 control chromosomes in the GnomAD database, including 18,002 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 0.46 (18002 hom., cov: 32)
• Consequence: SIDT1 NM_017699.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.417

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]

SIDT1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SIDT1	NM_017699.3	c.223-2941A>G		intron_variant		ENST00000264852.9	NP_060169.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SIDT1	ENST00000264852.9	c.223-2941A>G		intron_variant		2	NM_017699.3	ENSP00000264852.4
SIDT1	ENST00000393830.4	c.223-2941A>G		intron_variant		1		ENSP00000377416.4
SIDT1	ENST00000483946.1	n.68-2941A>G		intron_variant		4
SIDT1	ENST00000491730.5	n.690-2941A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70405 AN: 152028 Hom.: 17998 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.463 AC: 70429 AN: 152146 Hom.: 18002 Cov.: 32 AF XY: 0.462 AC XY: 34350 AN XY: 74390

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.589

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.521

Gnomad4 NFE AF: 0.562

Gnomad4 OTH AF: 0.491

Alfa AF: 0.522 Hom.: 4912

Bravo AF: 0.460

Asia WGS AF: 0.372 AC: 1293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.3
DANN	Benign	0.54

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: rs6769767; hg19: chr3-113282326;