rs4970357

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr1-1141684-C-A
• chr1-1141684-C-G
• chr1-1141684-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

LOC124903820 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01342	NR_038869.1	n.302+652C>A		intron_variant	Intron 2 of 2
LOC124903820	XR_007065351.1	n.75+12926C>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01342	ENST00000416774.1	n.302+652C>A		intron_variant	Intron 2 of 2	1

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

Gnomad4 AFR AF: 0.911

Gnomad4 AMR AF: 0.886

Gnomad4 ASJ AF: 0.894

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.792

Gnomad4 FIN AF: 0.874

Gnomad4 NFE AF: 0.905

Gnomad4 OTH AF: 0.874

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.78
DANN	Benign	0.76
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: rs4970357; hg19: chr1-1077064;