rs6921044

Variant names:

• chr6-140016306-C-T
• rs6921044
• ENST00000456896.6:n.81+39874C>T

Variant summary

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

The ENST00000456896.6(LINC02941):​n.81+39874C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.572 in 151,892 control chromosomes in the GnomAD database, including 26,404 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 0.57 (26404 hom., cov: 31)
• Consequence: LINC02941 ENST00000456896.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91
• Publications: 1 publications found

Genes affected

LINC02941 (HGNC:55956): (long intergenic non-protein coding RNA 2941)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000456896.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02941	NR_121622.1		n.114+39874C>T		intron	N/A
	LINC02941	NR_121623.1		n.114+39874C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02941	ENST00000456896.6	TSL:5	n.81+39874C>T		intron	N/A
	LINC02941	ENST00000656952.2		n.81+37879C>T		intron	N/A
	LINC02941	ENST00000664620.1		n.140+37879C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86728 AN: 151774 Hom.: 26373 Cov.: 31

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.572 AC: 86809 AN: 151892 Hom.: 26404 Cov.: 31 AF XY: 0.571 AC XY: 42364 AN XY: 74226

African (AFR) AF: 0.772 AC: 31983 AN: 41446

American (AMR) AF: 0.605 AC: 9245 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1529 AN: 3470

East Asian (EAS) AF: 0.562 AC: 2891 AN: 5148

South Asian (SAS) AF: 0.408 AC: 1960 AN: 4808

European-Finnish (FIN) AF: 0.537 AC: 5658 AN: 10536

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32055 AN: 67902

Other (OTH) AF: 0.509 AC: 1073 AN: 2108

Alfa AF: 0.486 Hom.: 28864

Bravo AF: 0.588

Asia WGS AF: 0.486 AC: 1687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.13
DANN	Benign	0.36
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs6921044; hg19: chr6-140337443;