rs7302017

Variant names:

• chr12-62610803-G-A
• rs7302017
• ENST00000550290.2:n.85-2802G>A

Variant summary

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

The ENST00000550290.2(MIRLET7IHG):​n.85-2802G>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 14 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MIRLET7IHG	NR_186001.1	n.94-2802G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIRLET7IHG	ENST00000550290.2	n.85-2802G>A		intron_variant	Intron 1 of 1	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

African (AFR) AF: 0.757 AC: 31394 AN: 41480

American (AMR) AF: 0.675 AC: 10317 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.908 AC: 3151 AN: 3472

East Asian (EAS) AF: 0.594 AC: 3075 AN: 5174

South Asian (SAS) AF: 0.734 AC: 3542 AN: 4824

European-Finnish (FIN) AF: 0.851 AC: 9008 AN: 10582

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.849 AC: 57752 AN: 68014

Other (OTH) AF: 0.805 AC: 1700 AN: 2112

Alfa AF: 0.827 Hom.: 163573

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
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs7302017; hg19: chr12-63004583;