rs351408

chr1-212267786-G-A

Variant summary

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

The ENST00000685933.1(LINC02608):n.90+17193C>T 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 0.29 in 152,092 control chromosomes in the GnomAD database, including 6,946 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 0.29 (6946 hom., cov: 32)
• Consequence: LINC02608 ENST00000685933.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50

Genes affected

LINC02608 (HGNC:54052): (long intergenic non-protein coding RNA 2608)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02608	NR_125984.1	n.43+17193C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02608	ENST00000685933.1	n.90+17193C>T		intron_variant, non_coding_transcript_variant
LINC02608	ENST00000691706.1	n.106+17193C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44024 AN: 151974 Hom.: 6949 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.290 AC: 44045 AN: 152092 Hom.: 6946 Cov.: 32 AF XY: 0.284 AC XY: 21152 AN XY: 74356

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.224

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.370

Gnomad4 OTH AF: 0.302

Alfa AF: 0.340 Hom.: 4435

Bravo AF: 0.290

Asia WGS AF: 0.239 AC: 830 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.16
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs351408; hg19: chr1-212441128;