rs7521783

chr1-150170994-T-C

Variant summary

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

The NR_135098.1(LINC02988):n.191-2736T>C 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 0.149 in 152,046 control chromosomes in the GnomAD database, including 1,825 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 0.15 (1825 hom., cov: 32)
• Consequence: LINC02988 NR_135098.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.489

Genes affected

LINC02988 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02988	NR_135098.1	n.191-2736T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22579 AN: 151928 Hom.: 1821 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.0972

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.000964

Gnomad SAS AF: 0.0288

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.149 AC: 22592 AN: 152046 Hom.: 1825 Cov.: 32 AF XY: 0.143 AC XY: 10641 AN XY: 74340

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.0971

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.000966

Gnomad4 SAS AF: 0.0291

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.125

Alfa AF: 0.156 Hom.: 955

Bravo AF: 0.144

Asia WGS AF: 0.0270 AC: 96 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.3
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7521783; hg19: chr1-150143193;