6-22694600-G-T

Variant names:

• chr6-22694600-G-T
• rs1555108
• ENST00000821964.1:n.277+23121C>A

Variant summary

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

The ENST00000821964.1(LINC03005):​n.277+23121C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.835 in 152,174 control chromosomes in the GnomAD database, including 53,389 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 0.83 (53389 hom., cov: 33)
• Consequence: LINC03005 ENST00000821964.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.465
• Publications: 5 publications found

Genes affected

LINC03005 (HGNC:):

LINC03005 (HGNC:56130): (long intergenic non-protein coding RNA 3005)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.914 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03005	NR_134613.1	n.204+23121C>A		intron_variant	Intron 1 of 1
LINC03005	NR_134614.1	n.204+23121C>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03005	ENST00000821964.1	n.277+23121C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.835 AC: 126891 AN: 152056 Hom.: 53331 Cov.: 33

Gnomad AFR AF: 0.921

Gnomad AMI AF: 0.950

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.780

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.800

Gnomad FIN AF: 0.825

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.820

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

GnomAD4 genome AF: 0.835 AC: 127010 AN: 152174 Hom.: 53389 Cov.: 33 AF XY: 0.835 AC XY: 62132 AN XY: 74386

African (AFR) AF: 0.921 AC: 38281 AN: 41554

American (AMR) AF: 0.867 AC: 13242 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.780 AC: 2708 AN: 3470

East Asian (EAS) AF: 0.652 AC: 3372 AN: 5168

South Asian (SAS) AF: 0.799 AC: 3855 AN: 4822

European-Finnish (FIN) AF: 0.825 AC: 8726 AN: 10576

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.794 AC: 53966 AN: 67988

Other (OTH) AF: 0.819 AC: 1730 AN: 2112

Alfa AF: 0.804 Hom.: 141794

Bravo AF: 0.844

Asia WGS AF: 0.732 AC: 2544 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.45
DANN	Benign	0.43
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs1555108; hg19: chr6-22694829;