rs4646298

chr5-132369527-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NR_110997.1(MIR3936HG):n.73+317G>A 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 0.0765 in 162,174 control chromosomes in the GnomAD database, including 616 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.076 (569 hom., cov: 32)
  • Exomes 𝑓: 0.079 (47 hom.)
• Consequence: MIR3936HG NR_110997.1 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.94

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BP6: Variant 5-132369527-C-T is Benign according to our data. Variant chr5-132369527-C-T is described in ClinVar as [Benign]. Clinvar id is 1236418.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR3936HG	NR_110997.1	n.73+317G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR3936HG	ENST00000621103.4	n.73+317G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0764 AC: 11621 AN: 152038 Hom.: 572 Cov.: 32

Gnomad AFR AF: 0.0616

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.0492

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.0651

Gnomad FIN AF: 0.0733

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0764

Gnomad OTH AF: 0.0762

GnomAD4 exome AF: 0.0792 AC: 793 AN: 10018 Hom.: 47 Cov.: 0 AF XY: 0.0771 AC XY: 399 AN XY: 5178

Gnomad4 AFR exome AF: 0.0698

Gnomad4 AMR exome AF: 0.0459

Gnomad4 ASJ exome AF: 0.0820

Gnomad4 EAS exome AF: 0.278

Gnomad4 SAS exome AF: 0.0612

Gnomad4 FIN exome AF: 0.0597

Gnomad4 NFE exome AF: 0.0684

Gnomad4 OTH exome AF: 0.102

GnomAD4 genome AF: 0.0764 AC: 11621 AN: 152156 Hom.: 569 Cov.: 32 AF XY: 0.0755 AC XY: 5617 AN XY: 74390

Gnomad4 AFR AF: 0.0616

Gnomad4 AMR AF: 0.0491

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.0650

Gnomad4 FIN AF: 0.0733

Gnomad4 NFE AF: 0.0764

Gnomad4 OTH AF: 0.0764

Alfa AF: 0.0769 Hom.: 66

Bravo AF: 0.0745

Asia WGS AF: 0.123 AC: 429 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 29, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	0.19
Dann	Benign	0.89
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4646298; hg19: chr5-131705219;