rs12482697

Variant names:

• chr21-33920895-T-G
• rs12482697
• ENST00000429238.2:c.-214-4918A>C

Variant summary

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

The ENST00000429238.2(ENSG00000249209):​c.-214-4918A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0779 in 152,232 control chromosomes in the GnomAD database, including 498 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 0.078 (498 hom., cov: 31)
• Consequence: ENSG00000249209 ENST00000429238.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290

Genes affected

ENSG00000249209 (HGNC:):

LINC00649 (HGNC:44305): (long intergenic non-protein coding RNA 649)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0914 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000249209	ENST00000429238.2	c.-214-4918A>C		intron_variant	Intron 1 of 7	5		ENSP00000394107.2

Frequencies

GnomAD3 genomes AF: 0.0778 AC: 11835 AN: 152114 Hom.: 499 Cov.: 31

Gnomad AFR AF: 0.0709

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.0551

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.00597

Gnomad SAS AF: 0.0768

Gnomad FIN AF: 0.0534

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0933

Gnomad OTH AF: 0.0847

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

GnomAD4 genome AF: 0.0779 AC: 11856 AN: 152232 Hom.: 498 Cov.: 31 AF XY: 0.0749 AC XY: 5573 AN XY: 74450

Gnomad4 AFR AF: 0.0712

Gnomad4 AMR AF: 0.0551

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.00579

Gnomad4 SAS AF: 0.0773

Gnomad4 FIN AF: 0.0534

Gnomad4 NFE AF: 0.0933

Gnomad4 OTH AF: 0.0838

Alfa AF: 0.0922 Hom.: 884

Bravo AF: 0.0789

Asia WGS AF: 0.0380 AC: 131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.9
DANN	Benign	0.79

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

Publications

LitVar

Other links and lift over

dbSNP: rs12482697; hg19: chr21-35293199;