chr5-172544483-C-A

Position:

• chr5-172544483-C-A

Variant summary

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

The ENST00000652199.1(LINC01944):​n.434-121G>T 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 0.113 in 152,226 control chromosomes in the GnomAD database, including 979 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 0.11 (979 hom., cov: 32)
• Consequence: LINC01944 ENST00000652199.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100

Genes affected

LINC01944 (HGNC:52768): (long intergenic non-protein coding RNA 1944)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01944	ENST00000652199.1	n.434-121G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17118 AN: 152108 Hom.: 976 Cov.: 32

Gnomad AFR AF: 0.0943

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0732

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.113 AC: 17127 AN: 152226 Hom.: 979 Cov.: 32 AF XY: 0.112 AC XY: 8335 AN XY: 74454

Gnomad4 AFR AF: 0.0942

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.0732

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.129

Alfa AF: 0.119 Hom.: 1483

Bravo AF: 0.112

Asia WGS AF: 0.125 AC: 434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.5
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1541918; hg19: chr5-171971486;