rs297941

Variant names:

• chr12-49925303-A-G
• rs297941
• ENST00000546821.5:n.2813A>G

Your query was ambiguous. Multiple possible variants found:

• chr12-49925303-A-G
• chr12-49925303-A-T

Variant summary

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

The ENST00000546821.5(LINC02395):​n.2813A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.537 in 152,134 control chromosomes in the GnomAD database, including 23,760 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 0.54 (23760 hom., cov: 32)
  • Exomes 𝑓: 0.31 (0 hom.)
• Consequence: LINC02395 ENST00000546821.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 16 publications found

Genes affected

LINC02395 (HGNC:53322): (long intergenic non-protein coding RNA 2395)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02395	NR_110048.1	n.2813A>G		non_coding_transcript_exon_variant	Exon 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02395	ENST00000546821.5	n.2813A>G		non_coding_transcript_exon_variant	Exon 5 of 6	1
LINC02395	ENST00000547443.1	n.88+216A>G		intron_variant	Intron 1 of 4	3
LINC02395	ENST00000547954.2	n.1085+216A>G		intron_variant	Intron 6 of 6	3

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81661 AN: 152000 Hom.: 23710 Cov.: 32

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.585

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.514

GnomAD4 exome AF: 0.313 AC: 5 AN: 16 Hom.: 0 Cov.: 0 AF XY: 0.300 AC XY: 3 AN XY: 10

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 2 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.200 AC: 2 AN: 10

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.537 AC: 81758 AN: 152118 Hom.: 23760 Cov.: 32 AF XY: 0.529 AC XY: 39322 AN XY: 74394

African (AFR) AF: 0.776 AC: 32187 AN: 41498

American (AMR) AF: 0.407 AC: 6223 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1927 AN: 3472

East Asian (EAS) AF: 0.532 AC: 2743 AN: 5156

South Asian (SAS) AF: 0.464 AC: 2240 AN: 4824

European-Finnish (FIN) AF: 0.362 AC: 3835 AN: 10596

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.453 AC: 30805 AN: 67974

Other (OTH) AF: 0.511 AC: 1079 AN: 2112

Alfa AF: 0.484 Hom.: 54982

Bravo AF: 0.553

Asia WGS AF: 0.468 AC: 1628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.14
DANN	Benign	0.34
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs297941; hg19: chr12-50319086;