rs60978556

Positions:

• chr5-132369654-C-A
• chr5-132369654-C-G

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_Strong BP6_Very_Strong BS2

The NR_110997.1(MIR3936HG):​n.73+190G>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 0.0104 in 302,636 control chromosomes in the GnomAD database, including 32 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0084 (16 hom., cov: 33)
  • Exomes 𝑓: 0.012 (16 hom.)
• Consequence: MIR3936HG NR_110997.1 intron, non_coding_transcript
• Clinical Significance: Likely benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: -2.60

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -16 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BP6: Variant 5-132369654-C-A is Benign according to our data. Variant chr5-132369654-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 1140554.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS2: High Homozygotes in GnomAd4 at 16 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR3936HG	NR_110997.1	n.73+190G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR3936HG	ENST00000621103.4	n.73+190G>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.00846 AC: 1287 AN: 152136 Hom.: 16 Cov.: 33

Gnomad AFR AF: 0.00193

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.00301

Gnomad ASJ AF: 0.000865

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00517

Gnomad FIN AF: 0.0179

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.0136

Gnomad OTH AF: 0.00765

GnomAD4 exome AF: 0.0124 AC: 1871 AN: 150386 Hom.: 16 Cov.: 0 AF XY: 0.0122 AC XY: 930 AN XY: 76182

Gnomad4 AFR exome AF: 0.00228

Gnomad4 AMR exome AF: 0.00345

Gnomad4 ASJ exome AF: 0.000197

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00912

Gnomad4 FIN exome AF: 0.0199

Gnomad4 NFE exome AF: 0.0147

Gnomad4 OTH exome AF: 0.0103

GnomAD4 genome AF: 0.00844 AC: 1285 AN: 152250 Hom.: 16 Cov.: 33 AF XY: 0.00822 AC XY: 612 AN XY: 74456

Gnomad4 AFR AF: 0.00192

Gnomad4 AMR AF: 0.00301

Gnomad4 ASJ AF: 0.000865

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00518

Gnomad4 FIN AF: 0.0179

Gnomad4 NFE AF: 0.0136

Gnomad4 OTH AF: 0.00757

Alfa AF: 0.00208 Hom.: 0

Bravo AF: 0.00736

Asia WGS AF: 0.00289 AC: 12 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Renal carnitine transport defect Benign:2

Likely benign, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Jul 19, 2021	- -
Likely benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 15, 2024	- -

not provided Benign:1

Likely benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

-

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	1.8
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs60978556; hg19: chr5-131705346;