chr2-65531391-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 19 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000377977.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02934	ENST00000377977.3	TSL:2	n.862+30244T>C		intron	N/A
	LINC02934	ENST00000606978.5	TSL:5	n.455+48239T>C		intron	N/A
	LINC02934	ENST00000661422.1		n.2253-19861T>C		intron	N/A

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

African (AFR) AF: 0.408 AC: 16917 AN: 41474

American (AMR) AF: 0.588 AC: 8985 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 1989 AN: 3470

East Asian (EAS) AF: 0.621 AC: 3204 AN: 5160

South Asian (SAS) AF: 0.724 AC: 3492 AN: 4826

European-Finnish (FIN) AF: 0.602 AC: 6365 AN: 10570

Middle Eastern (MID) AF: 0.551 AC: 161 AN: 292

European-Non Finnish (NFE) AF: 0.610 AC: 41498 AN: 67982

Other (OTH) AF: 0.549 AC: 1157 AN: 2108

Alfa AF: 0.581 Hom.: 43784

Bravo AF: 0.542

Asia WGS AF: 0.665 AC: 2310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.8
DANN	Benign	0.76
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs3845817; hg19: chr2-65758525;