rs867604

Positions:

• chr14-53786405-G-C

Variant summary

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

The NR_184212.1(LINC02331):​n.505+6849C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.895 in 152,190 control chromosomes in the GnomAD database, including 62,886 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 0.90 (62886 hom., cov: 31)
• Consequence: LINC02331 NR_184212.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.664

Genes affected

LINC02331 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.992 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02331	NR_184212.1	n.505+6849C>G		intron_variant
LINC02331	NR_184213.1	n.505+6849C>G		intron_variant
LINC02331	NR_184214.1	n.524+6849C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02331	ENST00000418927.2	n.580+6849C>G		intron_variant		5
ENSG00000237356	ENST00000649040.1	n.65+20686G>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.896 AC: 136215 AN: 152072 Hom.: 62877 Cov.: 31

Gnomad AFR AF: 0.638

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.960

Gnomad ASJ AF: 0.999

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.994

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.998

Gnomad OTH AF: 0.931

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

GnomAD4 genome AF: 0.895 AC: 136265 AN: 152190 Hom.: 62886 Cov.: 31 AF XY: 0.898 AC XY: 66851 AN XY: 74408

Gnomad4 AFR AF: 0.638

Gnomad4 AMR AF: 0.960

Gnomad4 ASJ AF: 0.999

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.995

Gnomad4 FIN AF: 1.00

Gnomad4 NFE AF: 0.998

Gnomad4 OTH AF: 0.931

Alfa AF: 0.936 Hom.: 8456

Bravo AF: 0.881

Asia WGS AF: 0.973 AC: 3384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	14
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs867604; hg19: chr14-54253123;