rs349410

Variant names:

• chr1-4417979-C-A
• rs349410
• ENST00000665284.1:n.725C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-4417979-C-A
• chr1-4417979-C-G

Variant summary

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

The ENST00000665284.1(LINC01777):​n.725C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.782 in 152,104 control chromosomes in the GnomAD database, including 46,987 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 0.78 (46987 hom., cov: 32)
• Consequence: LINC01777 ENST00000665284.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.210
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.886 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000665284.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01777	NR_027088.1		n.854+1431C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01777	ENST00000665284.1		n.725C>A		non_coding_transcript_exon	Exon 4 of 4
	LINC01777	ENST00000670434.1		n.998C>A		non_coding_transcript_exon	Exon 4 of 4
	LINC01777	ENST00000671656.1		n.642C>A		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.782 AC: 118901 AN: 151984 Hom.: 46939 Cov.: 32

Gnomad AFR AF: 0.893

Gnomad AMI AF: 0.802

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.805

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.756

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.782 AC: 119002 AN: 152104 Hom.: 46987 Cov.: 32 AF XY: 0.775 AC XY: 57640 AN XY: 74340

African (AFR) AF: 0.893 AC: 37087 AN: 41516

American (AMR) AF: 0.759 AC: 11604 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.805 AC: 2795 AN: 3472

East Asian (EAS) AF: 0.698 AC: 3602 AN: 5164

South Asian (SAS) AF: 0.657 AC: 3152 AN: 4800

European-Finnish (FIN) AF: 0.643 AC: 6793 AN: 10564

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.756 AC: 51422 AN: 67982

Other (OTH) AF: 0.771 AC: 1628 AN: 2112

Alfa AF: 0.770 Hom.: 19563

Bravo AF: 0.794

Asia WGS AF: 0.696 AC: 2422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.18
DANN	Benign	0.44
PhyloP100		-0.21

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs349410;

hg19: chr1-4478039;