rs6540731

chr1-212218821-G-A

Variant summary

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

The NR_125982.1(LINC02608):n.292-4045C>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 0.383 in 152,018 control chromosomes in the GnomAD database, including 11,436 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 0.38 (11436 hom., cov: 32)
• Consequence: LINC02608 NR_125982.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.520

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02608	NR_125982.1	n.292-4045C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02608	ENST00000685933.1	n.148-4045C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58183 AN: 151900 Hom.: 11423 Cov.: 32

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.383 AC: 58232 AN: 152018 Hom.: 11436 Cov.: 32 AF XY: 0.374 AC XY: 27827 AN XY: 74316

Gnomad4 AFR AF: 0.435

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.318

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.325

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.403

Gnomad4 OTH AF: 0.377

Alfa AF: 0.384 Hom.: 2780

Bravo AF: 0.389

Asia WGS AF: 0.285 AC: 992 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.9
Dann	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6540731; hg19: chr1-212392163;