ENST00000687158.2:n.520-794A>G

Variant names:

• chr6-43932970-T-C
• rs844294
• ENST00000687158.2:n.520-794A>G

Variant summary

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

The ENST00000687158.2(SCIRT):​n.520-794A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 151,950 control chromosomes in the GnomAD database, including 24,292 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 0.55 (24292 hom., cov: 31)
• Consequence: SCIRT ENST00000687158.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.44
• Publications: 5 publications found

Genes affected

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

LINC01512 (HGNC:51201): (long intergenic non-protein coding RNA 1512)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000687158.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01512	NR_024478.1		n.439-3394T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCIRT	ENST00000687158.2		n.520-794A>G		intron	N/A
	SCIRT	ENST00000687455.2		n.245-794A>G		intron	N/A
	SCIRT	ENST00000687843.1		n.593-794A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84193 AN: 151832 Hom.: 24248 Cov.: 31

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.555 AC: 84283 AN: 151950 Hom.: 24292 Cov.: 31 AF XY: 0.550 AC XY: 40878 AN XY: 74270

African (AFR) AF: 0.698 AC: 28900 AN: 41420

American (AMR) AF: 0.591 AC: 9031 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 1989 AN: 3470

East Asian (EAS) AF: 0.331 AC: 1704 AN: 5154

South Asian (SAS) AF: 0.403 AC: 1941 AN: 4820

European-Finnish (FIN) AF: 0.443 AC: 4677 AN: 10552

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.503 AC: 34205 AN: 67948

Other (OTH) AF: 0.566 AC: 1191 AN: 2104

Alfa AF: 0.523 Hom.: 26324

Bravo AF: 0.574

Asia WGS AF: 0.407 AC: 1418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.028
DANN	Benign	0.35
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs844294; hg19: chr6-43900707;