chr2-65440138-C-A

Variant names:

• chr2-65440138-C-A
• rs6740462
• ENST00000377977.3:n.153+3256C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000377977.3(LINC02934):​n.153+3256C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.783 in 152,410 control chromosomes in the GnomAD database, including 47,137 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 0.78 (47048 hom., cov: 32)
  • Exomes 𝑓: 0.72 (89 hom.)
• Consequence: LINC02934 ENST00000377977.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.313
• Publications: 45 publications found

Genes affected

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

ENSG00000234255 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.884 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105374780	NR_187887.1		n.795-53G>T		intron	N/A
	LOC105374780	NR_187888.1		n.896-53G>T		intron	N/A
	LOC105374780	NR_187889.1		n.1182-53G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02934	ENST00000377977.3	TSL:2	n.153+3256C>A		intron	N/A
	ENSG00000234255	ENST00000597541.6	TSL:5	n.939-53G>T		intron	N/A
	ENSG00000234255	ENST00000600508.6	TSL:5	n.1434-53G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.783 AC: 118972 AN: 151952 Hom.: 47001 Cov.: 32

Gnomad AFR AF: 0.892

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.736

Gnomad OTH AF: 0.800

GnomAD4 exome AF: 0.721 AC: 245 AN: 340 Hom.: 89 AF XY: 0.757 AC XY: 168 AN XY: 222

African (AFR) AF: 1.00 AC: 4 AN: 4

American (AMR) AF: 1.00 AC: 2 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.833 AC: 10 AN: 12

East Asian (EAS) AF: 0.875 AC: 21 AN: 24

South Asian (SAS) AF: 1.00 AC: 4 AN: 4

European-Finnish (FIN) AF: 0.318 AC: 7 AN: 22

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.725 AC: 187 AN: 258

Other (OTH) AF: 0.714 AC: 10 AN: 14

GnomAD4 genome AF: 0.783 AC: 119081 AN: 152070 Hom.: 47048 Cov.: 32 AF XY: 0.780 AC XY: 57950 AN XY: 74314

African (AFR) AF: 0.891 AC: 37012 AN: 41518

American (AMR) AF: 0.790 AC: 12069 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.774 AC: 2686 AN: 3472

East Asian (EAS) AF: 0.833 AC: 4314 AN: 5176

South Asian (SAS) AF: 0.826 AC: 3980 AN: 4816

European-Finnish (FIN) AF: 0.620 AC: 6541 AN: 10548

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.736 AC: 49990 AN: 67954

Other (OTH) AF: 0.803 AC: 1694 AN: 2110

Alfa AF: 0.762 Hom.: 98981

Bravo AF: 0.799

Asia WGS AF: 0.831 AC: 2891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	5.5
DANN	Benign	0.83
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs6740462; hg19: chr2-65667272;