chr3-113615386-A-C

Position:

• chr3-113615386-A-C

Variant summary

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

The NM_017699.3(SIDT1):​c.1967-714A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 152,118 control chromosomes in the GnomAD database, including 6,988 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 0.27 (6988 hom., cov: 32)
• Consequence: SIDT1 NM_017699.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.88

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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SIDT1	NM_017699.3	c.1967-714A>C		intron_variant		ENST00000264852.9	NP_060169.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SIDT1	ENST00000264852.9	c.1967-714A>C		intron_variant		2	NM_017699.3	ENSP00000264852	P4
SIDT1	ENST00000393830.4	c.1981+309A>C		intron_variant		1		ENSP00000377416	A2
SIDT1	ENST00000463226.1	n.817+309A>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41644 AN: 152002 Hom.: 6982 Cov.: 32

Gnomad AFR AF: 0.0706

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.274 AC: 41664 AN: 152118 Hom.: 6988 Cov.: 32 AF XY: 0.272 AC XY: 20209 AN XY: 74354

Gnomad4 AFR AF: 0.0704

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.260

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.286

Gnomad4 NFE AF: 0.374

Gnomad4 OTH AF: 0.306

Alfa AF: 0.348 Hom.: 13267

Bravo AF: 0.272

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	12
DANN	Benign	0.73

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: rs950357; hg19: chr3-113334233;