5-124210411-T-C

Position:

• chr5-124210411-T-C

Variant summary

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

The NR_125774.1(LINC01170):​n.490-147901A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 152,050 control chromosomes in the GnomAD database, including 18,498 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 0.43 (18498 hom., cov: 32)
• Consequence: LINC01170 NR_125774.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.439

Genes affected

LINC01170 (HGNC:49542): (long intergenic non-protein coding RNA 1170)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01170	NR_125774.1	n.490-147901A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01170	ENST00000628324.2	n.403-147901A>G		intron_variant, non_coding_transcript_variant		2
LINC01170	ENST00000653233.1	n.496-73091A>G		intron_variant, non_coding_transcript_variant
LINC01170	ENST00000657766.1	n.344-73091A>G		intron_variant, non_coding_transcript_variant
LINC01170	ENST00000662643.1	n.344-73091A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66020 AN: 151932 Hom.: 18439 Cov.: 32

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.435 AC: 66134 AN: 152050 Hom.: 18498 Cov.: 32 AF XY: 0.429 AC XY: 31902 AN XY: 74326

Gnomad4 AFR AF: 0.806

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.366

Gnomad4 SAS AF: 0.393

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.404

Alfa AF: 0.323 Hom.: 4867

Bravo AF: 0.459

Asia WGS AF: 0.421 AC: 1466 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	10
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs922556; hg19: chr5-123546104;