rs349403

Variant names:

• chr1-4413942-A-G
• rs349403
• ENST00000423197.2:n.582+1310A>G

Variant summary

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

The ENST00000423197.2(LINC01777):​n.582+1310A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,124 control chromosomes in the GnomAD database, including 1,226 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 0.12 (1226 hom., cov: 33)
• Consequence: LINC01777 ENST00000423197.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.231
• Publications: 2 publications found

Genes affected

LINC01777 (HGNC:52567): (long intergenic non-protein coding RNA 1777)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01777	NR_027088.1	n.582+1310A>G		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01777	ENST00000423197.2	n.582+1310A>G		intron_variant	Intron 1 of 5	2
LINC01777	ENST00000633821.2	n.254+1593A>G		intron_variant	Intron 1 of 3	4
LINC01777	ENST00000635002.1	n.323+1593A>G		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17878 AN: 152006 Hom.: 1226 Cov.: 33

Gnomad AFR AF: 0.0580

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.0774

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.118 AC: 17878 AN: 152124 Hom.: 1226 Cov.: 33 AF XY: 0.116 AC XY: 8598 AN XY: 74380

African (AFR) AF: 0.0579 AC: 2402 AN: 41502

American (AMR) AF: 0.103 AC: 1572 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 711 AN: 3464

East Asian (EAS) AF: 0.0772 AC: 400 AN: 5184

South Asian (SAS) AF: 0.150 AC: 722 AN: 4808

European-Finnish (FIN) AF: 0.104 AC: 1096 AN: 10582

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10549 AN: 67994

Other (OTH) AF: 0.129 AC: 273 AN: 2116

Alfa AF: 0.148 Hom.: 876

Bravo AF: 0.112

Asia WGS AF: 0.136 AC: 473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.5
DANN	Benign	0.59
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs349403; hg19: chr1-4474002;