chr8-63871986-A-G

Variant names:

• chr8-63871986-A-G
• rs10504368
• ENST00000521958.1:n.411-14875T>C

Variant summary

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

The ENST00000521958.1(LINC01414):​n.411-14875T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 152,142 control chromosomes in the GnomAD database, including 6,257 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 0.28 (6257 hom., cov: 32)
• Consequence: LINC01414 ENST00000521958.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.208
• Publications: 3 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01414	NR_125826.1	n.411-14875T>C		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01414	ENST00000521958.1	n.411-14875T>C		intron_variant	Intron 4 of 4	4
LINC01414	ENST00000523191.6	n.422-22991T>C		intron_variant	Intron 4 of 5	4
LINC01414	ENST00000524360.5	n.248-22991T>C		intron_variant	Intron 4 of 5	4

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42210 AN: 152024 Hom.: 6253 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.278 AC: 42227 AN: 152142 Hom.: 6257 Cov.: 32 AF XY: 0.282 AC XY: 20984 AN XY: 74364

African (AFR) AF: 0.199 AC: 8259 AN: 41532

American (AMR) AF: 0.400 AC: 6111 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 814 AN: 3466

East Asian (EAS) AF: 0.364 AC: 1880 AN: 5162

South Asian (SAS) AF: 0.232 AC: 1117 AN: 4818

European-Finnish (FIN) AF: 0.328 AC: 3470 AN: 10578

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.290 AC: 19718 AN: 68002

Other (OTH) AF: 0.273 AC: 576 AN: 2112

Alfa AF: 0.282 Hom.: 798

Bravo AF: 0.278

Asia WGS AF: 0.316 AC: 1100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.21
DANN	Benign	0.48
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs10504368; hg19: chr8-64784543;