6-158945229-T-C

Variant names:

• chr6-158945229-T-C
• rs12207795
• ENST00000795721.1:n.276-2817T>C

Variant summary

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

The ENST00000795721.1(LINC02901):​n.276-2817T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,124 control chromosomes in the GnomAD database, including 1,717 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 0.11 (1717 hom., cov: 31)
• Consequence: LINC02901 ENST00000795721.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130
• Publications: 13 publications found

Genes affected

LINC02901 (HGNC:21179): (long intergenic non-protein coding RNA 2901)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000795721.1. 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
	LINC02901	ENST00000795721.1		n.276-2817T>C		intron	N/A
	LINC02901	ENST00000795722.1		n.502-2817T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17295 AN: 152006 Hom.: 1706 Cov.: 31

Gnomad AFR AF: 0.0748

Gnomad AMI AF: 0.0516

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.0902

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.0758

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.114 AC: 17342 AN: 152124 Hom.: 1717 Cov.: 31 AF XY: 0.120 AC XY: 8911 AN XY: 74388

African (AFR) AF: 0.0753 AC: 3125 AN: 41510

American (AMR) AF: 0.282 AC: 4309 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 376 AN: 3470

East Asian (EAS) AF: 0.415 AC: 2146 AN: 5168

South Asian (SAS) AF: 0.194 AC: 933 AN: 4820

European-Finnish (FIN) AF: 0.0902 AC: 954 AN: 10578

Middle Eastern (MID) AF: 0.0959 AC: 28 AN: 292

European-Non Finnish (NFE) AF: 0.0758 AC: 5152 AN: 68002

Other (OTH) AF: 0.129 AC: 272 AN: 2110

Alfa AF: 0.115 Hom.: 518

Bravo AF: 0.133

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	7.7
DANN	Benign	0.79
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs12207795; hg19: chr6-159366261;