rs6923866

Variant names:

• chr6-43933447-T-C
• rs6923866
• ENST00000687158.2:n.520-1271A>G

Variant summary

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

The ENST00000687158.2(SCIRT):​n.520-1271A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 152,114 control chromosomes in the GnomAD database, including 7,165 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 0.30 (7165 hom., cov: 32)
• Consequence: SCIRT ENST00000687158.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26
• Publications: 8 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=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01512	NR_024478.1	n.439-2917T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCIRT	ENST00000687158.2	n.520-1271A>G		intron_variant	Intron 3 of 3
SCIRT	ENST00000687455.2	n.245-1271A>G		intron_variant	Intron 2 of 2
SCIRT	ENST00000687843.1	n.593-1271A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44873 AN: 151996 Hom.: 7135 Cov.: 32

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.295 AC: 44949 AN: 152114 Hom.: 7165 Cov.: 32 AF XY: 0.290 AC XY: 21541 AN XY: 74368

African (AFR) AF: 0.410 AC: 16998 AN: 41458

American (AMR) AF: 0.306 AC: 4684 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1206 AN: 3472

East Asian (EAS) AF: 0.150 AC: 775 AN: 5174

South Asian (SAS) AF: 0.206 AC: 992 AN: 4826

European-Finnish (FIN) AF: 0.194 AC: 2059 AN: 10600

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17264 AN: 67986

Other (OTH) AF: 0.325 AC: 685 AN: 2108

Alfa AF: 0.273 Hom.: 2293

Bravo AF: 0.312

Asia WGS AF: 0.214 AC: 743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	16
DANN	Benign	0.68
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs6923866; hg19: chr6-43901184;