2-65531391-T-C

Variant names:

• chr2-65531391-T-C
• rs3845817
• ENST00000377977.3:n.862+30244T>C

Variant summary

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

The ENST00000377977.3(LINC02934):​n.862+30244T>C variant causes a intron 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 ENST00000377977.3 intron
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02934	ENST00000377977.3	n.862+30244T>C		intron_variant	Intron 4 of 4	2
LINC02934	ENST00000606978.5	n.455+48239T>C		intron_variant	Intron 4 of 9	5
LINC02934	ENST00000661422.1	n.2253-19861T>C		intron_variant	Intron 1 of 1

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;