rs6577555

Variant names:

• chr1-9152228-A-C
• rs6577555
• ENST00000635687.1:n.387-393T>G

Your query was ambiguous. Multiple possible variants found:

• chr1-9152228-A-C
• chr1-9152228-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000635687.1(MIR34AHG):​n.387-393T>G variant causes a intron 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 ENST00000635687.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.81
• Publications: 8 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000635687.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR34AHG	NR_132742.1		n.333-393T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR34AHG	ENST00000635687.1	TSL:1	n.387-393T>G		intron	N/A
	MIR34AHG	ENST00000782879.1		n.464-12207T>G		intron	N/A
	MIR34AHG	ENST00000782880.1		n.339-12207T>G		intron	N/A

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

African (AFR) AF: 0.807 AC: 33482 AN: 41496

American (AMR) AF: 0.771 AC: 11789 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.717 AC: 2489 AN: 3470

East Asian (EAS) AF: 0.752 AC: 3897 AN: 5180

South Asian (SAS) AF: 0.696 AC: 3352 AN: 4814

European-Finnish (FIN) AF: 0.670 AC: 7099 AN: 10592

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.709 AC: 48201 AN: 67978

Other (OTH) AF: 0.736 AC: 1555 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.51
DANN	Benign	0.42
PhyloP100		-2.8

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6577555;

hg19: chr1-9212287;