rs1889976

Variant names:

• chr1-185267380-G-A
• rs1889976
• NM_017673.7:c.2442-3943G>A

Variant summary

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

The NM_017673.7(SWT1):​c.2442-3943G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 152,020 control chromosomes in the GnomAD database, including 21,930 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 0.52 (21930 hom., cov: 32)
• Consequence: SWT1 NM_017673.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15
• Publications: 5 publications found

Genes affected

SWT1 (HGNC:16785): (SWT1 RNA endoribonuclease homolog) Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SWT1	NM_017673.7	c.2442-3943G>A		intron_variant	Intron 16 of 18	ENST00000367500.9	NP_060143.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SWT1	ENST00000367500.9	c.2442-3943G>A		intron_variant	Intron 16 of 18	1	NM_017673.7	ENSP00000356470.4
SWT1	ENST00000367501.7	c.2442-3943G>A		intron_variant	Intron 16 of 18	2		ENSP00000356471.3

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78680 AN: 151898 Hom.: 21886 Cov.: 32

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.518 AC: 78779 AN: 152020 Hom.: 21930 Cov.: 32 AF XY: 0.515 AC XY: 38289 AN XY: 74304

African (AFR) AF: 0.741 AC: 30722 AN: 41468

American (AMR) AF: 0.471 AC: 7195 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1288 AN: 3470

East Asian (EAS) AF: 0.444 AC: 2298 AN: 5174

South Asian (SAS) AF: 0.479 AC: 2310 AN: 4818

European-Finnish (FIN) AF: 0.412 AC: 4346 AN: 10558

Middle Eastern (MID) AF: 0.449 AC: 131 AN: 292

European-Non Finnish (NFE) AF: 0.429 AC: 29145 AN: 67940

Other (OTH) AF: 0.453 AC: 955 AN: 2108

Alfa AF: 0.454 Hom.: 8544

Bravo AF: 0.535

Asia WGS AF: 0.430 AC: 1496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.5
DANN	Benign	0.66
PhyloP100		-2.1
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: rs1889976; hg19: chr1-185236512;