rs4970357

chr1-1141684-C-Achr1-1141684-C-Gchr1-1141684-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_038869.1(LINC01342):n.302+652C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.887 in 128,518 control chromosomes in the GnomAD database, including 50,963 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 0.89 (50963 hom., cov: 15)
• Consequence: LINC01342 NR_038869.1 intron, non_coding_transcript
• 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/exons	MANE	UniProt
LINC01342	NR_038869.1	n.302+652C>A		intron_variant, non_coding_transcript_variant
LOC124903820	XR_007065351.1	n.75+12926C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01342	ENST00000416774.1	n.302+652C>A		intron_variant, non_coding_transcript_variant		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;