rs1446546

Positions:

• chr2-13726405-C-A
• chr2-13726405-C-G

Variant summary

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

The ENST00000417751.5(LINC00276):​n.405+12782G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0598 in 152,028 control chromosomes in the GnomAD database, including 564 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 0.060 (564 hom., cov: 32)
• Consequence: LINC00276 ENST00000417751.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.316

Genes affected

LINC00276 (HGNC:38663): (long intergenic non-protein coding RNA 276)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373438	XR_922816.2	n.248-429C>A		intron_variant, non_coding_transcript_variant
LOC105373438	XR_001739295.1	n.1559-429C>A		intron_variant, non_coding_transcript_variant
LOC105373438	XR_922815.2	n.196-429C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00276	ENST00000417751.5	n.405+12782G>T		intron_variant, non_coding_transcript_variant		2
	ENST00000420828.1	n.146-429C>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0597 AC: 9067 AN: 151912 Hom.: 562 Cov.: 32

Gnomad AFR AF: 0.0436

Gnomad AMI AF: 0.0231

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.0941

Gnomad FIN AF: 0.0329

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0307

Gnomad OTH AF: 0.0705

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

GnomAD4 genome AF: 0.0598 AC: 9092 AN: 152028 Hom.: 564 Cov.: 32 AF XY: 0.0630 AC XY: 4679 AN XY: 74320

Gnomad4 AFR AF: 0.0439

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.308

Gnomad4 SAS AF: 0.0944

Gnomad4 FIN AF: 0.0329

Gnomad4 NFE AF: 0.0306

Gnomad4 OTH AF: 0.0717

Alfa AF: 0.0526 Hom.: 99

Bravo AF: 0.0700

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.36
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1446546; hg19: chr2-13866530;