rs4566790

Variant names:

• chr5-12577626-G-A
• rs4566790
• ENST00000505196.1:n.196+2574G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-12577626-G-A
• chr5-12577626-G-T

Variant summary

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

The ENST00000505196.1(LINC01194):​n.196+2574G>A variant causes a intron 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 ENST00000505196.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.591
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC01194	NR_033383.1	n.196+2574G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01194	ENST00000505196.1	n.196+2574G>A		intron_variant	Intron 1 of 3	1
LINC01194	ENST00000505877.6	n.217+2574G>A		intron_variant	Intron 1 of 2	1
LINC01194	ENST00000513051.7	n.239+2574G>A		intron_variant	Intron 1 of 3	1

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

African (AFR) AF: 0.378 AC: 15560 AN: 41206

American (AMR) AF: 0.0722 AC: 1096 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.0558 AC: 192 AN: 3442

East Asian (EAS) AF: 0.0758 AC: 382 AN: 5040

South Asian (SAS) AF: 0.0707 AC: 336 AN: 4752

European-Finnish (FIN) AF: 0.0313 AC: 330 AN: 10540

Middle Eastern (MID) AF: 0.0694 AC: 20 AN: 288

European-Non Finnish (NFE) AF: 0.0310 AC: 2095 AN: 67604

Other (OTH) AF: 0.109 AC: 226 AN: 2078

Alfa AF: 0.0727 Hom.: 2802

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
PhyloP100		-0.59
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs4566790; hg19: chr5-12577738;