rs7561692

chr2-45282678-T-C

Variant summary

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

The ENST00000658738.1(LINC01121):n.708+18306A>G 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 0.174 in 152,130 control chromosomes in the GnomAD database, including 2,730 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 0.17 (2730 hom., cov: 32)
• Consequence: LINC01121 ENST00000658738.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.719

Genes affected

LINC01121 (HGNC:49266): (long intergenic non-protein coding RNA 1121)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01121	ENST00000658738.1	n.708+18306A>G		intron_variant, non_coding_transcript_variant
LINC01121	ENST00000427020.6	n.704+18306A>G		intron_variant, non_coding_transcript_variant		3
LINC01121	ENST00000430650.2	n.716+18306A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26398 AN: 152010 Hom.: 2720 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0970

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.174 AC: 26431 AN: 152130 Hom.: 2730 Cov.: 32 AF XY: 0.174 AC XY: 12947 AN XY: 74374

Gnomad4 AFR AF: 0.252

Gnomad4 AMR AF: 0.0968

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.374

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.153

Alfa AF: 0.143 Hom.: 984

Bravo AF: 0.172

Asia WGS AF: 0.264 AC: 922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.66
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7561692; hg19: chr2-45509817;