rs1423435

Variant names:

• chr5-37904986-G-A
• rs1423435
• ENST00000513673.1:n.235-5318C>T

Variant summary

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

The ENST00000513673.1(LINC02117):​n.235-5318C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.537 in 151,864 control chromosomes in the GnomAD database, including 23,193 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 0.54 (23193 hom., cov: 31)
• Consequence: LINC02117 ENST00000513673.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 3 publications found

Genes affected

LINC02117 (HGNC:52972): (long intergenic non-protein coding RNA 2117)

GDNF-AS1 (HGNC:43592): (GDNF antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.69 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
LINC02117	ENST00000513673.1	n.235-5318C>T		intron_variant	Intron 3 of 3	4
GDNF-AS1	ENST00000637926.1	n.156-8544G>A		intron_variant	Intron 1 of 3	5
GDNF-AS1	ENST00000715998.1	n.254+30720G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81560 AN: 151746 Hom.: 23168 Cov.: 31

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.537 AC: 81619 AN: 151864 Hom.: 23193 Cov.: 31 AF XY: 0.536 AC XY: 39743 AN XY: 74180

African (AFR) AF: 0.697 AC: 28871 AN: 41438

American (AMR) AF: 0.513 AC: 7832 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1256 AN: 3468

East Asian (EAS) AF: 0.137 AC: 705 AN: 5146

South Asian (SAS) AF: 0.383 AC: 1844 AN: 4810

European-Finnish (FIN) AF: 0.569 AC: 5975 AN: 10504

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.495 AC: 33596 AN: 67926

Other (OTH) AF: 0.502 AC: 1056 AN: 2102

Alfa AF: 0.493 Hom.: 73145

Bravo AF: 0.537

Asia WGS AF: 0.285 AC: 995 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	8.1
DANN	Benign	0.61
PhyloP100		0.064

Splicing

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

Other links and lift over

dbSNP: rs1423435; hg19: chr5-37905088;