chr8-64113580-C-T

Variant names:

• chr8-64113580-C-T
• rs1385610
• ENST00000521958.1:n.410+19868G>A

Variant summary

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

The ENST00000521958.1(LINC01414):​n.410+19868G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0859 in 152,034 control chromosomes in the GnomAD database, including 743 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 0.086 (743 hom., cov: 32)
• Consequence: LINC01414 ENST00000521958.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.620
• Publications: 1 publications found

Genes affected

LINC01414 (HGNC:50707): (long intergenic non-protein coding RNA 1414)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01414	NR_125826.1	n.410+19868G>A		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01414	ENST00000521958.1	n.410+19868G>A		intron_variant	Intron 4 of 4	4
LINC01414	ENST00000523191.6	n.421+19868G>A		intron_variant	Intron 4 of 5	4
LINC01414	ENST00000524360.5	n.195+19868G>A		intron_variant	Intron 3 of 5	4

Frequencies

GnomAD3 genomes AF: 0.0860 AC: 13063 AN: 151918 Hom.: 744 Cov.: 32

Gnomad AFR AF: 0.0216

Gnomad AMI AF: 0.0430

Gnomad AMR AF: 0.0628

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0388

Gnomad FIN AF: 0.0817

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.0894

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

GnomAD4 genome AF: 0.0859 AC: 13054 AN: 152034 Hom.: 743 Cov.: 32 AF XY: 0.0808 AC XY: 6002 AN XY: 74316

African (AFR) AF: 0.0215 AC: 893 AN: 41498

American (AMR) AF: 0.0627 AC: 958 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 597 AN: 3470

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5172

South Asian (SAS) AF: 0.0386 AC: 186 AN: 4816

European-Finnish (FIN) AF: 0.0817 AC: 862 AN: 10556

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9275 AN: 67946

Other (OTH) AF: 0.0880 AC: 185 AN: 2102

Alfa AF: 0.104 Hom.: 1279

Bravo AF: 0.0830

Asia WGS AF: 0.0170 AC: 62 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.2
DANN	Benign	0.83
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs1385610; hg19: chr8-65026137;