chr4-117437743-T-C

Variant names:

• chr4-117437743-T-C
• rs4632732
• ENST00000422145.7:n.159+8976T>C

Variant summary

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

The ENST00000422145.7(LINC01378):​n.159+8976T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 151,488 control chromosomes in the GnomAD database, including 5,404 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 0.26 (5404 hom., cov: 30)
• Consequence: LINC01378 ENST00000422145.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0480
• Publications: 2 publications found

Genes affected

LINC01378 (HGNC:50645): (long intergenic non-protein coding RNA 1378)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000422145.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01378	NR_125757.1		n.157+8976T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01378	ENST00000422145.7	TSL:3	n.159+8976T>C		intron	N/A
	LINC01378	ENST00000437514.2	TSL:3	n.196+8976T>C		intron	N/A
	LINC01378	ENST00000626258.2	TSL:5	n.200+31378T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.257 AC: 38902 AN: 151370 Hom.: 5387 Cov.: 30

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.257 AC: 38968 AN: 151488 Hom.: 5404 Cov.: 30 AF XY: 0.253 AC XY: 18746 AN XY: 74026

African (AFR) AF: 0.351 AC: 14499 AN: 41282

American (AMR) AF: 0.174 AC: 2644 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1032 AN: 3464

East Asian (EAS) AF: 0.116 AC: 597 AN: 5128

South Asian (SAS) AF: 0.275 AC: 1322 AN: 4810

European-Finnish (FIN) AF: 0.191 AC: 2014 AN: 10558

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16072 AN: 67760

Other (OTH) AF: 0.269 AC: 565 AN: 2102

Alfa AF: 0.242 Hom.: 7779

Bravo AF: 0.258

Asia WGS AF: 0.230 AC: 802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.61
PhyloP100		0.048

Splicing

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

Other links and lift over

dbSNP: rs4632732; hg19: chr4-118358899;