1-207253220-A-T

Variant names:

• chr1-207253220-A-T
• rs1835307
• ENST00000417084.1:n.84+4070A>T

Variant summary

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

The ENST00000417084.1(LINC02942):​n.84+4070A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.653 in 151,990 control chromosomes in the GnomAD database, including 32,886 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 0.65 (32886 hom., cov: 32)
• Consequence: LINC02942 ENST00000417084.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 5 publications found

Genes affected

LINC02942 (HGNC:55957): (long intergenic non-protein coding RNA 2942)

ENSG00000296591 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02942	NR_186170.1	n.186+8684A>T		intron_variant	Intron 2 of 3
LOC107985251	XR_007066837.1	n.444+68466T>A		intron_variant	Intron 1 of 3
LOC107985251	XR_007066838.1	n.444+68466T>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02942	ENST00000417084.1	n.84+4070A>T		intron_variant	Intron 1 of 3	3
LINC02942	ENST00000634239.1	n.176+8684A>T		intron_variant	Intron 2 of 3	5
ENSG00000296591	ENST00000740658.1	n.116+68466T>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.653 AC: 99124 AN: 151872 Hom.: 32860 Cov.: 32

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.841

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.691

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

GnomAD4 genome AF: 0.653 AC: 99204 AN: 151990 Hom.: 32886 Cov.: 32 AF XY: 0.651 AC XY: 48334 AN XY: 74290

African (AFR) AF: 0.596 AC: 24706 AN: 41432

American (AMR) AF: 0.668 AC: 10209 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.841 AC: 2920 AN: 3470

East Asian (EAS) AF: 0.445 AC: 2304 AN: 5178

South Asian (SAS) AF: 0.574 AC: 2773 AN: 4830

European-Finnish (FIN) AF: 0.714 AC: 7543 AN: 10558

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.682 AC: 46322 AN: 67924

Other (OTH) AF: 0.688 AC: 1456 AN: 2116

Alfa AF: 0.672 Hom.: 4303

Bravo AF: 0.648

Asia WGS AF: 0.477 AC: 1661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.0
DANN	Benign	0.59
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1835307; hg19: chr1-207426565;