rs1886979

Variant names:

• chr6-43937164-G-A
• rs1886979
• ENST00000691600.1:n.1222G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-43937164-G-A
• chr6-43937164-G-T

Variant summary

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

The NR_024478.1(LINC01512):​n.1239G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 151,870 control chromosomes in the GnomAD database, including 27,593 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 0.60 (27593 hom., cov: 30)
• Consequence: LINC01512 NR_024478.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.909

Genes affected

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

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01512	NR_024478.1	n.1239G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01512	ENST00000691600.1	n.1222G>A		non_coding_transcript_exon_variant	Exon 2 of 2
SCIRT	ENST00000687158.2	n.520-4988C>T		intron_variant	Intron 3 of 3
SCIRT	ENST00000687455.1	n.234-4988C>T		intron_variant	Intron 2 of 2
SCIRT	ENST00000687843.1	n.593-4988C>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.599 AC: 90832 AN: 151752 Hom.: 27543 Cov.: 30

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.642

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.599 AC: 90937 AN: 151870 Hom.: 27593 Cov.: 30 AF XY: 0.593 AC XY: 44015 AN XY: 74226

Gnomad4 AFR AF: 0.656

Gnomad4 AMR AF: 0.700

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.485

Gnomad4 SAS AF: 0.466

Gnomad4 FIN AF: 0.491

Gnomad4 NFE AF: 0.575

Gnomad4 OTH AF: 0.614

Alfa AF: 0.596 Hom.: 4619

Bravo AF: 0.620

Asia WGS AF: 0.495 AC: 1723 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.36
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1886979; hg19: chr6-43904901;