chr3-113563479-A-G

Variant names:

• chr3-113563479-A-G
• rs6769767
• NM_017699.3:c.223-2941A>G

Variant summary

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

The NM_001322294.2(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_001322294.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.417
• Publications: 5 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001322294.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SIDT1	NM_017699.3	MANE Select	c.223-2941A>G		intron	N/A	NP_060169.2
	SIDT1	NM_001322294.2		c.223-2941A>G		intron	N/A	NP_001309223.1
	SIDT1	NM_001308350.2		c.223-2941A>G		intron	N/A	NP_001295279.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SIDT1	ENST00000264852.9	TSL:2 MANE Select	c.223-2941A>G		intron	N/A	ENSP00000264852.4
	SIDT1	ENST00000393830.5	TSL:1	c.223-2941A>G		intron	N/A	ENSP00000377416.4
	SIDT1	ENST00000950250.1		c.223-2941A>G		intron	N/A	ENSP00000620309.1

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

African (AFR) AF: 0.270 AC: 11202 AN: 41512

American (AMR) AF: 0.589 AC: 9000 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1647 AN: 3470

East Asian (EAS) AF: 0.191 AC: 988 AN: 5176

South Asian (SAS) AF: 0.445 AC: 2147 AN: 4824

European-Finnish (FIN) AF: 0.521 AC: 5509 AN: 10576

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.562 AC: 38236 AN: 67984

Other (OTH) AF: 0.491 AC: 1036 AN: 2108

Alfa AF: 0.534 Hom.: 9460

Bravo AF: 0.460

Asia WGS AF: 0.372 AC: 1293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.3
DANN	Benign	0.54
PhyloP100		0.42
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: rs6769767; hg19: chr3-113282326;