rs447292

Positions:

• chr16-24243631-A-G
• chr16-24243631-A-T

Variant summary

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

The ENST00000567127.1(LINC02194):​n.34-4201A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.668 in 151,986 control chromosomes in the GnomAD database, including 34,492 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 0.67 (34492 hom., cov: 31)
• Consequence: LINC02194 ENST00000567127.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0600

Genes affected

LINC02194 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02194	NR_146569.1	n.34-4201A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02194	ENST00000567127.1	n.34-4201A>G		intron_variant		3
LINC02194	ENST00000567624.1	n.53-3461A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.668 AC: 101397 AN: 151868 Hom.: 34462 Cov.: 31

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.670

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.668 AC: 101471 AN: 151986 Hom.: 34492 Cov.: 31 AF XY: 0.664 AC XY: 49321 AN XY: 74262

Gnomad4 AFR AF: 0.798

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.715

Gnomad4 EAS AF: 0.554

Gnomad4 SAS AF: 0.649

Gnomad4 FIN AF: 0.578

Gnomad4 NFE AF: 0.638

Gnomad4 OTH AF: 0.666

Alfa AF: 0.643 Hom.: 31284

Bravo AF: 0.668

Asia WGS AF: 0.590 AC: 2053 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.6
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs447292; hg19: chr16-24254952;