rs3845817

Positions:

• chr2-65531391-T-C

Variant summary

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

The ENST00000606978.5(LINC02934):​n.455+48239T>C 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 0.554 in 152,072 control chromosomes in the GnomAD database, including 24,083 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 0.55 (24083 hom., cov: 32)
• Consequence: LINC02934 ENST00000606978.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131

Genes affected

LINC02934 (HGNC:55913): (long intergenic non-protein coding RNA 2934)

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 (SAS) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02934	ENST00000606978.5	n.455+48239T>C		intron_variant, non_coding_transcript_variant		5
LINC02934	ENST00000377977.3	n.862+30244T>C		intron_variant, non_coding_transcript_variant		2
LINC02934	ENST00000661422.1	n.2253-19861T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84242 AN: 151954 Hom.: 24088 Cov.: 32

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.554 AC: 84246 AN: 152072 Hom.: 24083 Cov.: 32 AF XY: 0.558 AC XY: 41450 AN XY: 74316

Gnomad4 AFR AF: 0.408

Gnomad4 AMR AF: 0.588

Gnomad4 ASJ AF: 0.573

Gnomad4 EAS AF: 0.621

Gnomad4 SAS AF: 0.724

Gnomad4 FIN AF: 0.602

Gnomad4 NFE AF: 0.610

Gnomad4 OTH AF: 0.549

Alfa AF: 0.599 Hom.: 26469

Bravo AF: 0.542

Asia WGS AF: 0.665 AC: 2310 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	4.8
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3845817; hg19: chr2-65758525;