rs2249349

chr10-53020917-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000668157.1(LINC02672):n.270+1907G>A 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 0.499 in 152,026 control chromosomes in the GnomAD database, including 20,345 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 0.50 (20345 hom., cov: 32)
• Consequence: LINC02672 ENST00000668157.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110

Genes affected

LINC02672 (HGNC:54159): (long intergenic non-protein coding RNA 2672)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02672	ENST00000668157.1	n.270+1907G>A		intron_variant, non_coding_transcript_variant
LINC02672	ENST00000654808.1	n.251+1907G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.499 AC: 75768 AN: 151908 Hom.: 20338 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.499 AC: 75798 AN: 152026 Hom.: 20345 Cov.: 32 AF XY: 0.503 AC XY: 37340 AN XY: 74292

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.596

Gnomad4 ASJ AF: 0.554

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.644

Gnomad4 FIN AF: 0.593

Gnomad4 NFE AF: 0.582

Gnomad4 OTH AF: 0.525

Alfa AF: 0.563 Hom.: 13964

Bravo AF: 0.486

Asia WGS AF: 0.600 AC: 2085 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
Cadd	Benign	12
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2249349; hg19: chr10-54780677;