rs7561692

Variant names:

• chr2-45282678-T-C
• rs7561692
• ENST00000427020.6:n.704+18306A>G

Variant summary

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

The ENST00000427020.6(LINC01121):​n.704+18306A>G variant causes a intron 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 ENST00000427020.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.719
• Publications: 0 publications found

Genes affected

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

ENSG00000286728 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01121	ENST00000427020.6	n.704+18306A>G		intron_variant	Intron 2 of 7	3
LINC01121	ENST00000430650.2	n.716+18306A>G		intron_variant	Intron 2 of 2	3
LINC01121	ENST00000658738.1	n.708+18306A>G		intron_variant	Intron 2 of 6
ENSG00000286728	ENST00000716440.1	n.417-7805T>C		intron_variant	Intron 5 of 5

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

African (AFR) AF: 0.252 AC: 10475 AN: 41492

American (AMR) AF: 0.0968 AC: 1481 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 401 AN: 3472

East Asian (EAS) AF: 0.374 AC: 1935 AN: 5168

South Asian (SAS) AF: 0.143 AC: 688 AN: 4818

European-Finnish (FIN) AF: 0.195 AC: 2061 AN: 10588

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8993 AN: 67988

Other (OTH) AF: 0.153 AC: 322 AN: 2106

Alfa AF: 0.151 Hom.: 1571

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
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs7561692; hg19: chr2-45509817;