rs9381282

Variant names:

• chr6-44040588-C-A
• rs9381282
• ENST00000422059.5:n.156+33909G>T

Your query was ambiguous. Multiple possible variants found:

• chr6-44040588-C-A
• chr6-44040588-C-T

Variant summary

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

The ENST00000422059.5(SCIRT):​n.156+33909G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,142 control chromosomes in the GnomAD database, including 3,227 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 0.18 (3227 hom., cov: 32)
• Consequence: SCIRT ENST00000422059.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111
• Publications: 5 publications found

Genes affected

SCIRT (HGNC:55341): (stem cell inhibitory RNA transcript)

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 = 0.523 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000422059.5. 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
	SCIRT	NR_125864.1		n.156+33909G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCIRT	ENST00000422059.5	TSL:2	n.156+33909G>T		intron	N/A
	SCIRT	ENST00000652850.2		n.154+33909G>T		intron	N/A
	SCIRT	ENST00000687158.2		n.154+33909G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27359 AN: 152024 Hom.: 3222 Cov.: 32

Gnomad AFR AF: 0.0645

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.180 AC: 27375 AN: 152142 Hom.: 3227 Cov.: 32 AF XY: 0.187 AC XY: 13908 AN XY: 74384

African (AFR) AF: 0.0643 AC: 2671 AN: 41542

American (AMR) AF: 0.229 AC: 3505 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 716 AN: 3470

East Asian (EAS) AF: 0.540 AC: 2780 AN: 5152

South Asian (SAS) AF: 0.381 AC: 1830 AN: 4804

European-Finnish (FIN) AF: 0.211 AC: 2237 AN: 10592

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 12950 AN: 67970

Other (OTH) AF: 0.191 AC: 403 AN: 2114

Alfa AF: 0.192 Hom.: 12363

Bravo AF: 0.175

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.37
PhyloP100		-0.11

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9381282;

hg19: chr6-44008325;