rs6540731

Variant names:

• chr1-212218821-G-A
• rs6540731
• ENST00000685933.2:n.153-4045C>T

Variant summary

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

The NR_125982.1(LINC02608):​n.292-4045C>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.520
• Publications: 16 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_125982.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02608	NR_125982.1		n.292-4045C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02608	ENST00000685933.2		n.153-4045C>T		intron	N/A
	LINC02608	ENST00000771310.1		n.163-4045C>T		intron	N/A
	LINC02608	ENST00000771311.1		n.184-4045C>T		intron	N/A

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

African (AFR) AF: 0.435 AC: 18031 AN: 41440

American (AMR) AF: 0.326 AC: 4977 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1104 AN: 3472

East Asian (EAS) AF: 0.206 AC: 1068 AN: 5178

South Asian (SAS) AF: 0.325 AC: 1567 AN: 4818

European-Finnish (FIN) AF: 0.271 AC: 2858 AN: 10556

Middle Eastern (MID) AF: 0.291 AC: 85 AN: 292

European-Non Finnish (NFE) AF: 0.403 AC: 27414 AN: 67954

Other (OTH) AF: 0.377 AC: 794 AN: 2108

Alfa AF: 0.385 Hom.: 9053

Bravo AF: 0.389

Asia WGS AF: 0.285 AC: 992 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.9
DANN	Benign	0.28
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs6540731; hg19: chr1-212392163;