ENST00000608785.2:n.170+1042A>G

Variant names:

• chr4-184381092-T-C
• rs1124191
• ENST00000608785.2:n.170+1042A>G

Variant summary

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

The ENST00000608785.2(LINC02362):​n.170+1042A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.717 in 152,010 control chromosomes in the GnomAD database, including 39,848 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 0.72 (39848 hom., cov: 32)
• Consequence: LINC02362 ENST00000608785.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.192
• Publications: 6 publications found

Genes affected

LINC02362 (HGNC:53284): (long intergenic non-protein coding RNA 2362)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02362	NR_125933.1	n.173+1042A>G		intron_variant	Intron 1 of 6
LINC02362	NR_125934.1	n.173+1042A>G		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02362	ENST00000608785.2	n.170+1042A>G		intron_variant	Intron 1 of 6	3
LINC02362	ENST00000610683.5	n.170+1042A>G		intron_variant	Intron 1 of 5	5
LINC02362	ENST00000658007.1	n.170+1042A>G		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.718 AC: 108983 AN: 151890 Hom.: 39816 Cov.: 32

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.797

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.815

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.736

Gnomad OTH AF: 0.712

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

GnomAD4 genome AF: 0.717 AC: 109066 AN: 152010 Hom.: 39848 Cov.: 32 AF XY: 0.724 AC XY: 53843 AN XY: 74320

African (AFR) AF: 0.599 AC: 24804 AN: 41426

American (AMR) AF: 0.791 AC: 12081 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.708 AC: 2457 AN: 3470

East Asian (EAS) AF: 0.996 AC: 5173 AN: 5192

South Asian (SAS) AF: 0.816 AC: 3933 AN: 4822

European-Finnish (FIN) AF: 0.777 AC: 8191 AN: 10542

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.736 AC: 50002 AN: 67968

Other (OTH) AF: 0.712 AC: 1498 AN: 2104

Alfa AF: 0.732 Hom.: 6913

Bravo AF: 0.716

Asia WGS AF: 0.862 AC: 2996 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.5
DANN	Benign	0.64
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs1124191; hg19: chr4-185302246;