rs4566790

chr5-12577626-G-Achr5-12577626-G-T

Variant summary

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

The NR_033383.1(LINC01194):n.196+2574G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 151,028 control chromosomes in the GnomAD database, including 3,101 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 0.13 (3101 hom., cov: 32)
• Consequence: LINC01194 NR_033383.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.591

Genes affected

LINC01194 (HGNC:37171): (long intergenic non-protein coding RNA 1194)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01194	NR_033383.1	n.196+2574G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01194	ENST00000505196.1	n.196+2574G>A		intron_variant, non_coding_transcript_variant		1
LINC01194	ENST00000505877.5	n.196+2574G>A		intron_variant, non_coding_transcript_variant		1
LINC01194	ENST00000513051.6	n.223+2574G>A		intron_variant, non_coding_transcript_variant		1
LINC01194	ENST00000664069.1	n.217+2574G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20196 AN: 150908 Hom.: 3090 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0723

Gnomad ASJ AF: 0.0558

Gnomad EAS AF: 0.0758

Gnomad SAS AF: 0.0702

Gnomad FIN AF: 0.0313

Gnomad MID AF: 0.0752

Gnomad NFE AF: 0.0310

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.134 AC: 20251 AN: 151028 Hom.: 3101 Cov.: 32 AF XY: 0.131 AC XY: 9667 AN XY: 73806

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.0722

Gnomad4 ASJ AF: 0.0558

Gnomad4 EAS AF: 0.0758

Gnomad4 SAS AF: 0.0707

Gnomad4 FIN AF: 0.0313

Gnomad4 NFE AF: 0.0310

Gnomad4 OTH AF: 0.109

Alfa AF: 0.0501 Hom.: 680

Bravo AF: 0.148

Asia WGS AF: 0.0940 AC: 330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	3.0
Dann	Benign	0.18
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4566790; hg19: chr5-12577738;