rs273900

chr5-132358913-G-Achr5-132358913-G-Cchr5-132358913-G-T

Variant summary

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

The NR_110997.1(MIR3936HG):n.417+1167C>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 0.598 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 NR_110997.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.350

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR3936HG	NR_110997.1	n.417+1167C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR3936HG	ENST00000621103.4	n.417+1167C>T		intron_variant, non_coding_transcript_variant		1
MIR3936HG	ENST00000616965.1	n.57+1167C>T		intron_variant, non_coding_transcript_variant		5
MIR3936HG	ENST00000649993.1	n.741+6022C>T		intron_variant, non_coding_transcript_variant
MIR3936HG	ENST00000669845.1	n.186+7655C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.655

Gnomad4 AMR AF: 0.650

Gnomad4 ASJ AF: 0.584

Gnomad4 EAS AF: 0.330

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.490

Gnomad4 NFE AF: 0.604

Gnomad4 OTH AF: 0.612

Alfa AF: 0.586 Hom.: 6807

Bravo AF: 0.619

Asia WGS AF: 0.383 AC: 1334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.9
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs273900; hg19: chr5-131694606;