rs6743916

Variant names:

• chr2-58477314-G-A
• rs6743916
• ENST00000422723.6:n.263+48850G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-58477314-G-A
• chr2-58477314-G-C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000422723.6(LINC01122):​n.263+48850G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 151,992 control chromosomes in the GnomAD database, including 10,208 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 0.36 (10208 hom., cov: 33)
• Consequence: LINC01122 ENST00000422723.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.72
• Publications: 6 publications found

Genes affected

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

ENSG00000289529 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01122	ENST00000422723.6	n.263+48850G>A		intron_variant	Intron 2 of 10	3
LINC01122	ENST00000422793.4	n.134+15469G>A		intron_variant	Intron 2 of 6	5
LINC01122	ENST00000429095.6	n.195+15469G>A		intron_variant	Intron 2 of 5	4

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54093 AN: 151874 Hom.: 10191 Cov.: 33

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.356 AC: 54144 AN: 151992 Hom.: 10208 Cov.: 33 AF XY: 0.355 AC XY: 26403 AN XY: 74288

African (AFR) AF: 0.463 AC: 19179 AN: 41462

American (AMR) AF: 0.317 AC: 4846 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1344 AN: 3468

East Asian (EAS) AF: 0.467 AC: 2409 AN: 5156

South Asian (SAS) AF: 0.466 AC: 2249 AN: 4824

European-Finnish (FIN) AF: 0.255 AC: 2690 AN: 10534

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.299 AC: 20292 AN: 67960

Other (OTH) AF: 0.370 AC: 779 AN: 2108

Alfa AF: 0.318 Hom.: 25234

Bravo AF: 0.367

Asia WGS AF: 0.457 AC: 1587 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	9.8
DANN	Benign	0.79
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs6743916; hg19: chr2-58704449;