6-22709510-C-G

Variant names:

• chr6-22709510-C-G
• rs4712709
• ENST00000821964.1:n.277+8211G>C

Variant summary

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

The ENST00000821964.1(LINC03005):​n.277+8211G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 151,940 control chromosomes in the GnomAD database, including 22,787 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 0.55 (22787 hom., cov: 32)
• Consequence: LINC03005 ENST00000821964.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.54
• 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=-0.61).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03005	NR_134613.1	n.204+8211G>C		intron_variant	Intron 1 of 1
LINC03005	NR_134614.1	n.204+8211G>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03005	ENST00000821964.1	n.277+8211G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82725 AN: 151822 Hom.: 22751 Cov.: 32

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.545 AC: 82811 AN: 151940 Hom.: 22787 Cov.: 32 AF XY: 0.548 AC XY: 40699 AN XY: 74262

African (AFR) AF: 0.495 AC: 20513 AN: 41424

American (AMR) AF: 0.589 AC: 8993 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 1534 AN: 3468

East Asian (EAS) AF: 0.750 AC: 3867 AN: 5156

South Asian (SAS) AF: 0.615 AC: 2957 AN: 4810

European-Finnish (FIN) AF: 0.609 AC: 6435 AN: 10560

Middle Eastern (MID) AF: 0.486 AC: 142 AN: 292

European-Non Finnish (NFE) AF: 0.544 AC: 36952 AN: 67958

Other (OTH) AF: 0.512 AC: 1077 AN: 2104

Alfa AF: 0.438 Hom.: 1279

Bravo AF: 0.537

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	14
DANN	Benign	0.61
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs4712709; hg19: chr6-22709739;