rs6719884

Variant names:

• chr2-58809781-A-C
• rs6719884
• ENST00000422723.6:n.326-40649A>C

Your query was ambiguous. Multiple possible variants found:

• chr2-58809781-A-C
• chr2-58809781-A-G

Variant summary

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

The ENST00000422723.6(LINC01122):​n.326-40649A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.563 in 151,920 control chromosomes in the GnomAD database, including 24,135 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 0.56 (24135 hom., cov: 32)
• Consequence: LINC01122 ENST00000422723.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.655
• Publications: 6 publications found

Genes affected

LINC01122 (HGNC:49267): (long intergenic non-protein coding RNA 1122)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01122	NR_033873.1	n.248-40649A>C		intron_variant	Intron 2 of 13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01122	ENST00000422723.6	n.326-40649A>C		intron_variant	Intron 3 of 10	3
LINC01122	ENST00000422793.4	n.197-40649A>C		intron_variant	Intron 3 of 6	5
LINC01122	ENST00000427421.5	n.248-40649A>C		intron_variant	Intron 2 of 13	2

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85427 AN: 151802 Hom.: 24114 Cov.: 32

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.706

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.563 AC: 85488 AN: 151920 Hom.: 24135 Cov.: 32 AF XY: 0.561 AC XY: 41622 AN XY: 74232

African (AFR) AF: 0.541 AC: 22429 AN: 41440

American (AMR) AF: 0.565 AC: 8616 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.626 AC: 2173 AN: 3470

East Asian (EAS) AF: 0.463 AC: 2381 AN: 5140

South Asian (SAS) AF: 0.644 AC: 3100 AN: 4816

European-Finnish (FIN) AF: 0.495 AC: 5225 AN: 10564

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.582 AC: 39498 AN: 67924

Other (OTH) AF: 0.576 AC: 1217 AN: 2114

Alfa AF: 0.575 Hom.: 54593

Bravo AF: 0.565

Asia WGS AF: 0.615 AC: 2138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.2
DANN	Benign	0.81
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs6719884; hg19: chr2-59036916;