rs4869272

chr5-96203744-C-T

Variant summary

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

The NR_130776.1(LOC101929710):n.37-104980C>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 0.723 in 151,878 control chromosomes in the GnomAD database, including 39,849 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 0.72 (39849 hom., cov: 31)
• Consequence: LOC101929710 NR_130776.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71

Genes affected

(HGNC:):

MIR583HG (HGNC:53061): (MIR583 host gene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101929710	NR_130776.1	n.37-104980C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000502645.2	n.37-104980C>T		intron_variant, non_coding_transcript_variant		5
MIR583HG	ENST00000507997.1	n.160-11231C>T		intron_variant, non_coding_transcript_variant		2
	ENST00000511775.1	n.36-114729C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109610 AN: 151760 Hom.: 39792 Cov.: 31

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.809

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.723 AC: 109734 AN: 151878 Hom.: 39849 Cov.: 31 AF XY: 0.724 AC XY: 53704 AN XY: 74204

Gnomad4 AFR AF: 0.787

Gnomad4 AMR AF: 0.773

Gnomad4 ASJ AF: 0.700

Gnomad4 EAS AF: 0.676

Gnomad4 SAS AF: 0.654

Gnomad4 FIN AF: 0.682

Gnomad4 NFE AF: 0.687

Gnomad4 OTH AF: 0.732

Alfa AF: 0.691 Hom.: 83858

Bravo AF: 0.730

Asia WGS AF: 0.691 AC: 2400 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.0030
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4869272; hg19: chr5-95539448;