rs6921044

chr6-140016306-C-T

Variant summary

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

The NR_121622.1(LINC02941):n.114+39874C>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 0.572 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 NR_121622.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91

Genes affected

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

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 (AFR) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02941	NR_121622.1	n.114+39874C>T		intron_variant, non_coding_transcript_variant
LINC02941	NR_121623.1	n.114+39874C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02941	ENST00000456896.6	n.81+39874C>T		intron_variant, non_coding_transcript_variant		5
LINC02941	ENST00000656952.1	n.69+37879C>T		intron_variant, non_coding_transcript_variant
LINC02941	ENST00000664620.1	n.140+37879C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.772

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.562

Gnomad4 SAS AF: 0.408

Gnomad4 FIN AF: 0.537

Gnomad4 NFE AF: 0.472

Gnomad4 OTH AF: 0.509

Alfa AF: 0.483 Hom.: 24128

Bravo AF: 0.588

Asia WGS AF: 0.486 AC: 1687 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	0.13
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6921044; hg19: chr6-140337443;