chr5-125233645-T-C

Position:

• chr5-125233645-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+64019T>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 0.742 in 151,802 control chromosomes in the GnomAD database, including 42,143 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 0.74 (42143 hom., cov: 31)
• Consequence: LOC101927421 NR_109882.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.700

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101927421	NR_109882.1	n.377+64019T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02240	ENST00000647105.1	n.288-91707T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.742 AC: 112580 AN: 151682 Hom.: 42104 Cov.: 31

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.874

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.746

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.742 AC: 112669 AN: 151802 Hom.: 42143 Cov.: 31 AF XY: 0.737 AC XY: 54664 AN XY: 74156

Gnomad4 AFR AF: 0.819

Gnomad4 AMR AF: 0.696

Gnomad4 ASJ AF: 0.746

Gnomad4 EAS AF: 0.524

Gnomad4 SAS AF: 0.639

Gnomad4 FIN AF: 0.717

Gnomad4 NFE AF: 0.731

Gnomad4 OTH AF: 0.760

Alfa AF: 0.731 Hom.: 38642

Bravo AF: 0.743

Asia WGS AF: 0.590 AC: 2054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.18
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1439609; hg19: chr5-124569338;