chr5-125208637-T-C

Position:

• chr5-125208637-T-C

Variant summary

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

The NR_109882.1(LOC101927421):​n.377+39011T>C 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 0.884 in 151,958 control chromosomes in the GnomAD database, including 59,993 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 0.88 (59993 hom., cov: 30)
• Consequence: LOC101927421 NR_109882.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01

Genes affected

LINC02240 (HGNC:53118): (long intergenic non-protein coding RNA 2240)

LOC101927421 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927421	NR_109882.1	n.377+39011T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02240	ENST00000647105.1	n.288-116715T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.884 AC: 134231 AN: 151840 Hom.: 59950 Cov.: 30

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.987

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.960

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.905

Gnomad FIN AF: 0.918

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.958

Gnomad OTH AF: 0.899

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

GnomAD4 genome AF: 0.884 AC: 134321 AN: 151958 Hom.: 59993 Cov.: 30 AF XY: 0.879 AC XY: 65272 AN XY: 74242

Gnomad4 AFR AF: 0.798

Gnomad4 AMR AF: 0.804

Gnomad4 ASJ AF: 0.960

Gnomad4 EAS AF: 0.671

Gnomad4 SAS AF: 0.906

Gnomad4 FIN AF: 0.918

Gnomad4 NFE AF: 0.958

Gnomad4 OTH AF: 0.899

Alfa AF: 0.919 Hom.: 39220

Bravo AF: 0.871

Asia WGS AF: 0.793 AC: 2758 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.21
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6595593; hg19: chr5-124544330;