chr5-87136800-T-C

Position:

• chr5-87136800-T-C

Variant summary

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

The NR_105018.1(LOC101929380):​n.48-654T>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 0.168 in 152,132 control chromosomes in the GnomAD database, including 2,659 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 0.17 (2659 hom., cov: 31)
• Consequence: LOC101929380 NR_105018.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.662

Genes affected

(HGNC:):

MIR4280HG (HGNC:54975): (MIR4280 host gene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101929380	NR_105018.1	n.48-654T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000503349.1	n.344-654T>C		intron_variant, non_coding_transcript_variant		2
MIR4280HG	ENST00000662995.1	n.148+1450A>G		intron_variant, non_coding_transcript_variant
	ENST00000515750.1	n.48-654T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25522 AN: 152016 Hom.: 2659 Cov.: 31

Gnomad AFR AF: 0.0400

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.168 AC: 25515 AN: 152132 Hom.: 2659 Cov.: 31 AF XY: 0.170 AC XY: 12655 AN XY: 74376

Gnomad4 AFR AF: 0.0399

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.228

Gnomad4 EAS AF: 0.237

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.163

Alfa AF: 0.210 Hom.: 5005

Bravo AF: 0.162

Asia WGS AF: 0.204 AC: 709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	3.7
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2032794; hg19: chr5-86432617;