5-174469021-G-C

Position:

• chr5-174469021-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000507361.5(LINC01411):​n.335+41271G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.698 in 151,512 control chromosomes in the GnomAD database, including 37,622 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 0.70 (37622 hom., cov: 31)
• Consequence: LINC01411 ENST00000507361.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.991

Genes affected

LINC01411 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01411	NR_125806.1	n.335+41271G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01411	ENST00000507361.5	n.335+41271G>C		intron_variant		3
LINC01411	ENST00000510234.5	n.194+41271G>C		intron_variant		3
LINC01411	ENST00000515513.5	n.394+41271G>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.698 AC: 105724 AN: 151394 Hom.: 37606 Cov.: 31

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.867

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.726

Gnomad NFE AF: 0.722

Gnomad OTH AF: 0.706

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

GnomAD4 genome AF: 0.698 AC: 105772 AN: 151512 Hom.: 37622 Cov.: 31 AF XY: 0.706 AC XY: 52261 AN XY: 74064

Gnomad4 AFR AF: 0.569

Gnomad4 AMR AF: 0.788

Gnomad4 ASJ AF: 0.642

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.867

Gnomad4 FIN AF: 0.720

Gnomad4 NFE AF: 0.722

Gnomad4 OTH AF: 0.710

Alfa AF: 0.711 Hom.: 4833

Bravo AF: 0.696

Asia WGS AF: 0.917 AC: 3177 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.52
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1087518; hg19: chr5-173896024;