rs7611694

Variant names:

• chr3-113556777-A-C
• rs7611694
• NM_017699.3:c.223-9643A>C

Your query was ambiguous. Multiple possible variants found:

• chr3-113556777-A-C
• chr3-113556777-A-T

Variant summary

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

The NM_017699.3(SIDT1):​c.223-9643A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 149,516 control chromosomes in the GnomAD database, including 12,800 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 0.40 (12800 hom., cov: 27)
• Consequence: SIDT1 NM_017699.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.276
• Publications: 52 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 (EAS) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017699.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SIDT1	NM_017699.3	MANE Select	c.223-9643A>C		intron	N/A	NP_060169.2	Q9NXL6-1
	SIDT1	NM_001322294.2		c.223-9643A>C		intron	N/A	NP_001309223.1
	SIDT1	NM_001308350.2		c.223-9643A>C		intron	N/A	NP_001295279.1	Q9NXL6-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SIDT1	ENST00000264852.9	TSL:2 MANE Select	c.223-9643A>C		intron	N/A	ENSP00000264852.4	Q9NXL6-1
	SIDT1	ENST00000393830.5	TSL:1	c.223-9643A>C		intron	N/A	ENSP00000377416.4	Q9NXL6-2
	SIDT1	ENST00000950250.1		c.223-9643A>C		intron	N/A	ENSP00000620309.1

Frequencies

GnomAD3 genomes AF: 0.403 AC: 60219 AN: 149416 Hom.: 12783 Cov.: 27

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.403 AC: 60274 AN: 149516 Hom.: 12800 Cov.: 27 AF XY: 0.409 AC XY: 29689 AN XY: 72592

African (AFR) AF: 0.349 AC: 14193 AN: 40622

American (AMR) AF: 0.331 AC: 4979 AN: 15048

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1395 AN: 3456

East Asian (EAS) AF: 0.723 AC: 3671 AN: 5076

South Asian (SAS) AF: 0.485 AC: 2306 AN: 4756

European-Finnish (FIN) AF: 0.514 AC: 4901 AN: 9528

Middle Eastern (MID) AF: 0.339 AC: 99 AN: 292

European-Non Finnish (NFE) AF: 0.407 AC: 27583 AN: 67732

Other (OTH) AF: 0.356 AC: 746 AN: 2098

Alfa AF: 0.402 Hom.: 39990

Bravo AF: 0.388

Asia WGS AF: 0.541 AC: 1880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.52
PhyloP100		0.28
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: rs7611694; hg19: chr3-113275624;