5-132358913-G-A

Variant names:

• chr5-132358913-G-A
• rs273900
• ENST00000621103.4:n.417+1167C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000621103.4(MIR3936HG):​n.417+1167C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.598 in 152,080 control chromosomes in the GnomAD database, including 27,746 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 0.60 (27746 hom., cov: 32)
• Consequence: MIR3936HG ENST00000621103.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.350
• Publications: 14 publications found

Genes affected

MIR3936HG (HGNC:40538): (MIR3936 host gene)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000621103.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR3936HG	NR_110997.1		n.417+1167C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR3936HG	ENST00000621103.4	TSL:1	n.417+1167C>T		intron	N/A
	MIR3936HG	ENST00000616965.1	TSL:5	n.57+1167C>T		intron	N/A
	MIR3936HG	ENST00000649993.1		n.741+6022C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.598 AC: 90800 AN: 151962 Hom.: 27717 Cov.: 32

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.598 AC: 90882 AN: 152080 Hom.: 27746 Cov.: 32 AF XY: 0.587 AC XY: 43623 AN XY: 74340

African (AFR) AF: 0.655 AC: 27162 AN: 41482

American (AMR) AF: 0.650 AC: 9936 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 2025 AN: 3466

East Asian (EAS) AF: 0.330 AC: 1706 AN: 5170

South Asian (SAS) AF: 0.358 AC: 1728 AN: 4822

European-Finnish (FIN) AF: 0.490 AC: 5176 AN: 10572

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.604 AC: 41020 AN: 67970

Other (OTH) AF: 0.612 AC: 1286 AN: 2102

Alfa AF: 0.594 Hom.: 9177

Bravo AF: 0.619

Asia WGS AF: 0.383 AC: 1334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.9
DANN	Benign	0.65
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs273900; hg19: chr5-131694606;