chr5-12652720-T-C

Variant names:

• chr5-12652720-T-C
• rs7721328
• ENST00000505196.1:n.278+56942T>C

Variant summary

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

The ENST00000505196.1(LINC01194):​n.278+56942T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 151,984 control chromosomes in the GnomAD database, including 3,568 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 0.21 (3568 hom., cov: 33)
• Consequence: LINC01194 ENST00000505196.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250
• Publications: 2 publications found

Genes affected

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

ENSG00000309222 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01194	NR_033383.1	n.278+56942T>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01194	ENST00000505196.1	n.278+56942T>C		intron_variant	Intron 2 of 3	1
LINC01194	ENST00000505877.6	n.300-1927T>C		intron_variant	Intron 2 of 2	1
LINC01194	ENST00000513051.7	n.321+56942T>C		intron_variant	Intron 2 of 3	1

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31788 AN: 151866 Hom.: 3566 Cov.: 33

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.0996

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.209 AC: 31814 AN: 151984 Hom.: 3568 Cov.: 33 AF XY: 0.209 AC XY: 15501 AN XY: 74308

African (AFR) AF: 0.238 AC: 9885 AN: 41480

American (AMR) AF: 0.252 AC: 3836 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 570 AN: 3470

East Asian (EAS) AF: 0.430 AC: 2224 AN: 5176

South Asian (SAS) AF: 0.310 AC: 1495 AN: 4826

European-Finnish (FIN) AF: 0.0996 AC: 1051 AN: 10554

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12085 AN: 67916

Other (OTH) AF: 0.202 AC: 427 AN: 2112

Alfa AF: 0.176 Hom.: 1412

Bravo AF: 0.224

Asia WGS AF: 0.350 AC: 1207 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.42
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs7721328; hg19: chr5-12652832;