5-12786868-C-T

Variant names:

• chr5-12786868-C-T
• rs10073652
• ENST00000505196.1:n.381-17336C>T

Variant summary

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

The XR_007058695.1(LOC124900941):​n.2687G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 151,602 control chromosomes in the GnomAD database, including 5,480 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 0.25 (5480 hom., cov: 32)
• Consequence: LOC124900941 XR_007058695.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.793
• Publications: 4 publications found

Genes affected

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

LOC124900941 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000505196.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01194	NR_033383.1		n.381-18072C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01194	ENST00000505196.1	TSL:1	n.381-17336C>T		intron	N/A
	LINC01194	ENST00000839367.1		n.378-70929C>T		intron	N/A
	LINC01194	ENST00000839368.1		n.377-18072C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37127 AN: 151484 Hom.: 5470 Cov.: 32

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.245 AC: 37177 AN: 151602 Hom.: 5480 Cov.: 32 AF XY: 0.249 AC XY: 18409 AN XY: 74080

African (AFR) AF: 0.383 AC: 15861 AN: 41378

American (AMR) AF: 0.241 AC: 3664 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 419 AN: 3464

East Asian (EAS) AF: 0.437 AC: 2246 AN: 5142

South Asian (SAS) AF: 0.355 AC: 1710 AN: 4816

European-Finnish (FIN) AF: 0.165 AC: 1745 AN: 10560

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10869 AN: 67750

Other (OTH) AF: 0.226 AC: 476 AN: 2104

Alfa AF: 0.189 Hom.: 10426

Bravo AF: 0.256

Asia WGS AF: 0.359 AC: 1249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.0
DANN	Benign	0.84
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs10073652; hg19: chr5-12786980;