12-49915969-G-A

Position:

• chr12-49915969-G-A

Variant summary

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

The ENST00000546821.5(LINC02395):​n.131+3886G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.029 in 152,080 control chromosomes in the GnomAD database, including 191 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 0.029 (191 hom., cov: 32)
• Consequence: LINC02395 ENST00000546821.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142

Genes affected

LINC02395 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0963 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02395	NR_110048.1	n.131+3886G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02395	ENST00000546821.5	n.131+3886G>A		intron_variant		1
LINC02395	ENST00000547954.2	n.407-7656G>A		intron_variant		3
LINC02395	ENST00000549734.1	n.104+3886G>A		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.0290 AC: 4412 AN: 151964 Hom.: 192 Cov.: 32

Gnomad AFR AF: 0.0990

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0151

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000415

Gnomad FIN AF: 0.000189

Gnomad MID AF: 0.00641

Gnomad NFE AF: 0.000441

Gnomad OTH AF: 0.0244

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

GnomAD4 genome AF: 0.0290 AC: 4415 AN: 152080 Hom.: 191 Cov.: 32 AF XY: 0.0284 AC XY: 2109 AN XY: 74358

Gnomad4 AFR AF: 0.0988

Gnomad4 AMR AF: 0.0150

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000415

Gnomad4 FIN AF: 0.000189

Gnomad4 NFE AF: 0.000441

Gnomad4 OTH AF: 0.0242

Alfa AF: 0.0216 Hom.: 16

Bravo AF: 0.0342

Asia WGS AF: 0.00289 AC: 10 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.97
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs297903; hg19: chr12-50309752;