rs4327597

Positions:

• chr5-12755900-A-G
• chr5-12755900-A-T

Variant summary

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

The NR_033383.1(LINC01194):​n.380+44601A>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 0.791 in 152,002 control chromosomes in the GnomAD database, including 48,227 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 0.79 (48227 hom., cov: 32)
• Consequence: LINC01194 NR_033383.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.329

Genes affected

LINC01194 (HGNC:37171): (long intergenic non-protein coding RNA 1194)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01194	NR_033383.1	n.380+44601A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01194	ENST00000505196.1	n.380+44601A>G		intron_variant, non_coding_transcript_variant		1
LINC01194	ENST00000513051.6	n.408-3459A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.791 AC: 120119 AN: 151886 Hom.: 48203 Cov.: 32

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.833

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.848

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.853

Gnomad OTH AF: 0.799

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

GnomAD4 genome AF: 0.791 AC: 120190 AN: 152002 Hom.: 48227 Cov.: 32 AF XY: 0.790 AC XY: 58691 AN XY: 74324

Gnomad4 AFR AF: 0.683

Gnomad4 AMR AF: 0.853

Gnomad4 ASJ AF: 0.833

Gnomad4 EAS AF: 0.533

Gnomad4 SAS AF: 0.753

Gnomad4 FIN AF: 0.848

Gnomad4 NFE AF: 0.853

Gnomad4 OTH AF: 0.798

Alfa AF: 0.832 Hom.: 12343

Bravo AF: 0.786

Asia WGS AF: 0.669 AC: 2323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4327597; hg19: chr5-12756012;