rs7611694

chr3-113556777-A-Cchr3-113556777-A-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SIDT1	NM_017699.3	c.223-9643A>C		intron_variant		ENST00000264852.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SIDT1	ENST00000264852.9	c.223-9643A>C		intron_variant		2	NM_017699.3	P4
SIDT1	ENST00000393830.4	c.223-9643A>C		intron_variant		1		A2
SIDT1	ENST00000483946.1	n.68-9643A>C		intron_variant, non_coding_transcript_variant		4
SIDT1	ENST00000491730.5	n.690-9643A>C		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.331

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.723

Gnomad4 SAS AF: 0.485

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.407

Gnomad4 OTH AF: 0.356

Alfa AF: 0.393 Hom.: 16939

Bravo AF: 0.388

Asia WGS AF: 0.541 AC: 1880 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	1.5
Dann	Benign	0.52

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: rs7611694; hg19: chr3-113275624;