rs77585961

Positions:

• chr1-9151409-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NR_132742.1(MIR34AHG):​n.759G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0342 in 340,962 control chromosomes in the GnomAD database, including 274 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 0.033 (109 hom., cov: 32)
  • Exomes 𝑓: 0.035 (165 hom.)
• Consequence: MIR34AHG NR_132742.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.351

Genes affected

MIR34AHG (HGNC:51913): (MIR34A host gene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0331 (5039/152322) while in subpopulation NFE AF= 0.0483 (3288/68022). AF 95% confidence interval is 0.047. There are 109 homozygotes in gnomad4. There are 2411 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 109 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR34AHG	NR_132742.1	n.759G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR34AHG	ENST00000635687.1	n.813G>A		non_coding_transcript_exon_variant	2/2	1

Frequencies

GnomAD3 genomes AF: 0.0331 AC: 5042 AN: 152204 Hom.: 109 Cov.: 32

Gnomad AFR AF: 0.00924

Gnomad AMI AF: 0.0505

Gnomad AMR AF: 0.0453

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0108

Gnomad FIN AF: 0.0351

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0483

Gnomad OTH AF: 0.0416

GnomAD4 exome AF: 0.0351 AC: 6626 AN: 188640 Hom.: 165 Cov.: 0 AF XY: 0.0322 AC XY: 3347 AN XY: 103954

Gnomad4 AFR exome AF: 0.00782

Gnomad4 AMR exome AF: 0.0397

Gnomad4 ASJ exome AF: 0.0286

Gnomad4 EAS exome AF: 0.000275

Gnomad4 SAS exome AF: 0.0120

Gnomad4 FIN exome AF: 0.0398

Gnomad4 NFE exome AF: 0.0460

Gnomad4 OTH exome AF: 0.0352

GnomAD4 genome AF: 0.0331 AC: 5039 AN: 152322 Hom.: 109 Cov.: 32 AF XY: 0.0324 AC XY: 2411 AN XY: 74498

Gnomad4 AFR AF: 0.00921

Gnomad4 AMR AF: 0.0452

Gnomad4 ASJ AF: 0.0297

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0110

Gnomad4 FIN AF: 0.0351

Gnomad4 NFE AF: 0.0483

Gnomad4 OTH AF: 0.0407

Alfa AF: 0.0435 Hom.: 34

Bravo AF: 0.0331

Asia WGS AF: 0.00982 AC: 34 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.1
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs77585961; hg19: chr1-9211468;