6-140139871-G-C

Variant names:

• chr6-140139871-G-C
• rs169291
• XR_943069.2:n.1195C>G

Variant summary

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

The XR_943069.2(LOC105378025):​n.1195C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.822 in 152,140 control chromosomes in the GnomAD database, including 52,138 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 0.82 (52138 hom., cov: 32)
• Consequence: LOC105378025 XR_943069.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.167
• Publications: 1 publications found

Genes affected

LOC105378025 (HGNC:):

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.945 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000725932.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02941	ENST00000725932.1		n.653-5995G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.822 AC: 124925 AN: 152022 Hom.: 52073 Cov.: 32

Gnomad AFR AF: 0.953

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.845

Gnomad ASJ AF: 0.816

Gnomad EAS AF: 0.941

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.729

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.822 AC: 125049 AN: 152140 Hom.: 52138 Cov.: 32 AF XY: 0.823 AC XY: 61228 AN XY: 74354

African (AFR) AF: 0.953 AC: 39581 AN: 41548

American (AMR) AF: 0.845 AC: 12927 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.816 AC: 2830 AN: 3468

East Asian (EAS) AF: 0.941 AC: 4854 AN: 5160

South Asian (SAS) AF: 0.804 AC: 3871 AN: 4812

European-Finnish (FIN) AF: 0.734 AC: 7746 AN: 10558

Middle Eastern (MID) AF: 0.733 AC: 214 AN: 292

European-Non Finnish (NFE) AF: 0.745 AC: 50672 AN: 67994

Other (OTH) AF: 0.809 AC: 1705 AN: 2108

Alfa AF: 0.690 Hom.: 1962

Bravo AF: 0.838

Asia WGS AF: 0.878 AC: 3049 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.53
DANN	Benign	0.62
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs169291; hg19: chr6-140461008;