3-113581336-A-T

Position:

• chr3-113581336-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.664-25A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.442 in 1,591,484 control chromosomes in the GnomAD database, including 159,831 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. There are indicators that this mutation may affect the branch point..

• Frequency:
  • Genomes: 𝑓 0.46 (17044 hom., cov: 31)
  • Exomes 𝑓: 0.44 (142787 hom.)
• Consequence: SIDT1 NM_017699.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264

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: This place is a probable branch point but likely benign (scored 3 / 10). Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SIDT1	NM_017699.3	c.664-25A>T		intron_variant		ENST00000264852.9	NP_060169.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SIDT1	ENST00000264852.9	c.664-25A>T		intron_variant		2	NM_017699.3	ENSP00000264852.4
SIDT1	ENST00000393830.4	c.664-25A>T		intron_variant		1		ENSP00000377416.4
SIDT1	ENST00000491730.5	n.1131-25A>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70496 AN: 151650 Hom.: 17021 Cov.: 31

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.423

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.449

GnomAD3 exomes AF: 0.461 AC: 115464 AN: 250654 Hom.: 27844 AF XY: 0.460 AC XY: 62294 AN XY: 135436

Gnomad AFR exome AF: 0.522

Gnomad AMR exome AF: 0.359

Gnomad ASJ exome AF: 0.481

Gnomad EAS exome AF: 0.773

Gnomad SAS exome AF: 0.476

Gnomad FIN exome AF: 0.482

Gnomad NFE exome AF: 0.423

Gnomad OTH exome AF: 0.451

GnomAD4 exome AF: 0.439 AC: 632503 AN: 1439714 Hom.: 142787 Cov.: 27 AF XY: 0.441 AC XY: 316160 AN XY: 717648

Gnomad4 AFR exome AF: 0.528

Gnomad4 AMR exome AF: 0.368

Gnomad4 ASJ exome AF: 0.473

Gnomad4 EAS exome AF: 0.804

Gnomad4 SAS exome AF: 0.476

Gnomad4 FIN exome AF: 0.486

Gnomad4 NFE exome AF: 0.419

Gnomad4 OTH exome AF: 0.457

GnomAD4 genome AF: 0.465 AC: 70569 AN: 151770 Hom.: 17044 Cov.: 31 AF XY: 0.468 AC XY: 34686 AN XY: 74164

Gnomad4 AFR AF: 0.519

Gnomad4 AMR AF: 0.378

Gnomad4 ASJ AF: 0.489

Gnomad4 EAS AF: 0.777

Gnomad4 SAS AF: 0.475

Gnomad4 FIN AF: 0.479

Gnomad4 NFE AF: 0.425

Gnomad4 OTH AF: 0.444

Alfa AF: 0.459 Hom.: 3022

Bravo AF: 0.461

Asia WGS AF: 0.556 AC: 1935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.8
DANN	Benign	0.71
BranchPoint Hunter		3.0

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: rs2271494; hg19: chr3-113300183;