rs7302017

Positions:

• chr12-62610803-G-A

Variant summary

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

The ENST00000550290.2(MIRLET7IHG):​n.85-2802G>A 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 0.795 in 152,136 control chromosomes in the GnomAD database, including 48,611 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 0.80 (48611 hom., cov: 32)
• Consequence: MIRLET7IHG ENST00000550290.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59

Genes affected

MIRLET7IHG (HGNC:55478): (MIRLET7I host gene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIRLET7IHG	ENST00000550290.2	n.85-2802G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.795 AC: 120860 AN: 152018 Hom.: 48567 Cov.: 32

Gnomad AFR AF: 0.757

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.851

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.849

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.795 AC: 120958 AN: 152136 Hom.: 48611 Cov.: 32 AF XY: 0.790 AC XY: 58732 AN XY: 74364

Gnomad4 AFR AF: 0.757

Gnomad4 AMR AF: 0.675

Gnomad4 ASJ AF: 0.908

Gnomad4 EAS AF: 0.594

Gnomad4 SAS AF: 0.734

Gnomad4 FIN AF: 0.851

Gnomad4 NFE AF: 0.849

Gnomad4 OTH AF: 0.805

Alfa AF: 0.833 Hom.: 65641

Bravo AF: 0.780

Asia WGS AF: 0.670 AC: 2332 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	0.26
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7302017; hg19: chr12-63004583;