ENST00000416774.1:n.302+652C>A

Variant names:

• chr1-1141684-C-A
• rs4970357
• ENST00000416774.1:n.302+652C>A

Variant summary

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

The ENST00000416774.1(LINC01342):​n.302+652C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.89 (50963 hom., cov: 15)
• Consequence: LINC01342 ENST00000416774.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800
• Publications: 4 publications found

Genes affected

LINC01342 (HGNC:50551): (long intergenic non-protein coding RNA 1342)

LOC124903820 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000416774.1. 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
	LINC01342	NR_038869.1		n.302+652C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01342	ENST00000416774.1	TSL:1	n.302+652C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.887 AC: 113923 AN: 128424 Hom.: 50915 Cov.: 15

Gnomad AFR AF: 0.911

Gnomad AMI AF: 0.981

Gnomad AMR AF: 0.886

Gnomad ASJ AF: 0.894

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.791

Gnomad FIN AF: 0.874

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.905

Gnomad OTH AF: 0.872

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

GnomAD4 genome AF: 0.887 AC: 114017 AN: 128518 Hom.: 50963 Cov.: 15 AF XY: 0.885 AC XY: 54610 AN XY: 61692

African (AFR) AF: 0.911 AC: 29402 AN: 32278

American (AMR) AF: 0.886 AC: 11547 AN: 13038

Ashkenazi Jewish (ASJ) AF: 0.894 AC: 2874 AN: 3214

East Asian (EAS) AF: 0.552 AC: 2360 AN: 4278

South Asian (SAS) AF: 0.792 AC: 2883 AN: 3638

European-Finnish (FIN) AF: 0.874 AC: 7300 AN: 8352

Middle Eastern (MID) AF: 0.826 AC: 195 AN: 236

European-Non Finnish (NFE) AF: 0.905 AC: 55203 AN: 60996

Other (OTH) AF: 0.874 AC: 1535 AN: 1756

Alfa AF: 0.869 Hom.: 2768

Bravo AF: 0.890

Asia WGS AF: 0.710 AC: 2468 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.78
DANN	Benign	0.76
PhyloP100		-0.0080
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

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

Other links and lift over

dbSNP: rs4970357;

hg19: chr1-1077064;