4-4850446-C-G

Variant names:

• chr4-4850446-C-G
• rs868257
• ENST00000609099.1:n.407-261C>G

Variant summary

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

The ENST00000609099.1(LINC01396):​n.407-261C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 152,050 control chromosomes in the GnomAD database, including 3,656 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 0.21 (3656 hom., cov: 32)
• Consequence: LINC01396 ENST00000609099.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.597
• Publications: 1 publications found

Genes affected

LINC01396 (HGNC:50675): (long intergenic non-protein coding RNA 1396)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01396	NR_125765.1	n.407-261C>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01396	ENST00000609099.1	n.407-261C>G		intron_variant	Intron 3 of 3	3
LINC01396	ENST00000652410.1	n.1227-261C>G		intron_variant	Intron 3 of 3
LINC01396	ENST00000662851.1	n.1137-261C>G		intron_variant	Intron 1 of 1
LINC01396	ENST00000724736.1	n.368-261C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32275 AN: 151932 Hom.: 3650 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.212 AC: 32292 AN: 152050 Hom.: 3656 Cov.: 32 AF XY: 0.216 AC XY: 16053 AN XY: 74318

African (AFR) AF: 0.141 AC: 5845 AN: 41500

American (AMR) AF: 0.200 AC: 3061 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 699 AN: 3470

East Asian (EAS) AF: 0.262 AC: 1348 AN: 5144

South Asian (SAS) AF: 0.345 AC: 1660 AN: 4810

European-Finnish (FIN) AF: 0.240 AC: 2534 AN: 10566

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.244 AC: 16584 AN: 67958

Other (OTH) AF: 0.212 AC: 449 AN: 2114

Alfa AF: 0.146 Hom.: 289

Bravo AF: 0.202

Asia WGS AF: 0.270 AC: 938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.73
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs868257; hg19: chr4-4852173;