rs6577555

chr1-9152228-A-Cchr1-9152228-A-T

Variant summary

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

The NR_132742.1(MIR34AHG):n.333-393T>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 0.741 in 152,130 control chromosomes in the GnomAD database, including 41,952 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 0.74 (41952 hom., cov: 32)
• Consequence: MIR34AHG NR_132742.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.81

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR34AHG	NR_132742.1	n.333-393T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR34AHG	ENST00000635687.1	n.387-393T>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.741 AC: 112614 AN: 152012 Hom.: 41887 Cov.: 32

Gnomad AFR AF: 0.806

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.733

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.741 AC: 112737 AN: 152130 Hom.: 41952 Cov.: 32 AF XY: 0.737 AC XY: 54777 AN XY: 74354

Gnomad4 AFR AF: 0.807

Gnomad4 AMR AF: 0.771

Gnomad4 ASJ AF: 0.717

Gnomad4 EAS AF: 0.752

Gnomad4 SAS AF: 0.696

Gnomad4 FIN AF: 0.670

Gnomad4 NFE AF: 0.709

Gnomad4 OTH AF: 0.736

Alfa AF: 0.651 Hom.: 2086

Bravo AF: 0.753

Asia WGS AF: 0.748 AC: 2604 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.51
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6577555; hg19: chr1-9212287;