rs4862396

Variant names:

• chr4-184622518-T-C
• rs4862396
• ENST00000519173.1:n.204+2221A>G

Variant summary

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

The ENST00000519173.1(LINC02365):​n.204+2221A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,144 control chromosomes in the GnomAD database, including 1,240 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 0.12 (1240 hom., cov: 32)
• Consequence: LINC02365 ENST00000519173.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.302
• Publications: 15 publications found

Genes affected

LINC02365 (HGNC:53285): (long intergenic non-protein coding RNA 2365)

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 (AMR) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02365	NR_131965.1	n.171+904A>G		intron_variant	Intron 2 of 2
LINC02365	NR_131966.1	n.134+2221A>G		intron_variant	Intron 1 of 1
LINC02365	NR_131967.1	n.134+2221A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02365	ENST00000519173.1	n.204+2221A>G		intron_variant	Intron 1 of 1	3
LINC02365	ENST00000520280.2	n.507+904A>G		intron_variant	Intron 3 of 3	3
LINC02365	ENST00000522554.2	n.600+2221A>G		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17636 AN: 152026 Hom.: 1243 Cov.: 32

Gnomad AFR AF: 0.0478

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.0775

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.116 AC: 17621 AN: 152144 Hom.: 1240 Cov.: 32 AF XY: 0.114 AC XY: 8462 AN XY: 74366

African (AFR) AF: 0.0477 AC: 1980 AN: 41514

American (AMR) AF: 0.169 AC: 2588 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 527 AN: 3470

East Asian (EAS) AF: 0.114 AC: 588 AN: 5180

South Asian (SAS) AF: 0.126 AC: 605 AN: 4802

European-Finnish (FIN) AF: 0.0775 AC: 822 AN: 10602

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10054 AN: 67982

Other (OTH) AF: 0.129 AC: 273 AN: 2110

Alfa AF: 0.141 Hom.: 5042

Bravo AF: 0.121

Asia WGS AF: 0.118 AC: 411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.55
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs4862396; hg19: chr4-185543672;