rs7949144

chr11-64890927-G-C

Variant summary

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

The NR_133640.1(MIR194-2HG):n.277-1587C>G 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 0.0394 in 243,176 control chromosomes in the GnomAD database, including 300 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 0.040 (173 hom., cov: 31)
  • Exomes 𝑓: 0.039 (127 hom.)
• Consequence: MIR194-2HG NR_133640.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.75

Genes affected

MIR194-2HG (HGNC:51946): (MIR194-2 host gene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.0536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR194-2HG	NR_133640.1	n.277-1587C>G		intron_variant, non_coding_transcript_variant
MIR194-2HG	NR_133638.1	n.2280C>G		non_coding_transcript_exon_variant	2/2
MIR194-2HG	NR_133639.1	n.437+1502C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR194-2HG	ENST00000710930.1	n.551+1502C>G		intron_variant, non_coding_transcript_variant
MIR194-2HG	ENST00000413053.2	n.2280C>G		non_coding_transcript_exon_variant	2/2	2
MIR194-2HG	ENST00000710929.1	n.391-1587C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0400 AC: 6082 AN: 152132 Hom.: 173 Cov.: 31

Gnomad AFR AF: 0.0104

Gnomad AMI AF: 0.0516

Gnomad AMR AF: 0.0378

Gnomad ASJ AF: 0.0942

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0126

Gnomad FIN AF: 0.0948

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0513

Gnomad OTH AF: 0.0469

GnomAD4 exome AF: 0.0386 AC: 3507 AN: 90926 Hom.: 127 Cov.: 0 AF XY: 0.0354 AC XY: 1791 AN XY: 50602

Gnomad4 AFR exome AF: 0.00783

Gnomad4 AMR exome AF: 0.0293

Gnomad4 ASJ exome AF: 0.0962

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0144

Gnomad4 FIN exome AF: 0.0826

Gnomad4 NFE exome AF: 0.0434

Gnomad4 OTH exome AF: 0.0492

GnomAD4 genome AF: 0.0399 AC: 6081 AN: 152250 Hom.: 173 Cov.: 31 AF XY: 0.0413 AC XY: 3071 AN XY: 74430

Gnomad4 AFR AF: 0.0104

Gnomad4 AMR AF: 0.0377

Gnomad4 ASJ AF: 0.0942

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0124

Gnomad4 FIN AF: 0.0948

Gnomad4 NFE AF: 0.0512

Gnomad4 OTH AF: 0.0464

Alfa AF: 0.0479 Hom.: 24

Bravo AF: 0.0351

Asia WGS AF: 0.00895 AC: 31 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	9.0
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7949144; hg19: chr11-64658399;