22-46113303-C-T

Variant names:

• chr22-46113303-C-T
• rs7288847
• XM_047441694.1:c.*8714C>T

Variant summary

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

The ENST00000360737.4(MIRLET7BHG):​n.3935C>T 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 0.568 in 182,778 control chromosomes in the GnomAD database, including 32,793 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 0.55 (25937 hom., cov: 34)
  • Exomes 𝑓: 0.66 (6856 hom.)
• Consequence: MIRLET7BHG ENST00000360737.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720
• Publications: 6 publications found

Genes affected

LOC124905135 (HGNC:):

MIRLET7BHG (HGNC:37189): (MIRLET7B host gene)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000360737.4. 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
	MIRLET7BHG	NR_027033.2		n.4092C>T		non_coding_transcript_exon	Exon 6 of 6
	MIRLET7BHG	NR_110479.1		n.3941C>T		non_coding_transcript_exon	Exon 5 of 5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIRLET7BHG	ENST00000360737.4	TSL:2	n.3935C>T		non_coding_transcript_exon	Exon 5 of 5
	MIRLET7BHG	ENST00000794300.1		n.1163C>T		non_coding_transcript_exon	Exon 6 of 6
	MIRLET7BHG	ENST00000794301.1		n.1044C>T		non_coding_transcript_exon	Exon 6 of 6

Frequencies

GnomAD3 genomes AF: 0.550 AC: 83697 AN: 152052 Hom.: 25914 Cov.: 34

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.572

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.973

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.599

GnomAD4 exome AF: 0.657 AC: 20120 AN: 30608 Hom.: 6856 Cov.: 0 AF XY: 0.661 AC XY: 10805 AN XY: 16346

African (AFR) AF: 0.252 AC: 125 AN: 496

American (AMR) AF: 0.664 AC: 1831 AN: 2758

Ashkenazi Jewish (ASJ) AF: 0.705 AC: 444 AN: 630

East Asian (EAS) AF: 0.973 AC: 1035 AN: 1064

South Asian (SAS) AF: 0.690 AC: 3317 AN: 4804

European-Finnish (FIN) AF: 0.655 AC: 783 AN: 1196

Middle Eastern (MID) AF: 0.675 AC: 81 AN: 120

European-Non Finnish (NFE) AF: 0.640 AC: 11500 AN: 17964

Other (OTH) AF: 0.637 AC: 1004 AN: 1576

GnomAD4 genome AF: 0.550 AC: 83747 AN: 152170 Hom.: 25937 Cov.: 34 AF XY: 0.556 AC XY: 41327 AN XY: 74386

African (AFR) AF: 0.263 AC: 10910 AN: 41538

American (AMR) AF: 0.633 AC: 9680 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2381 AN: 3472

East Asian (EAS) AF: 0.973 AC: 5019 AN: 5158

South Asian (SAS) AF: 0.698 AC: 3369 AN: 4830

European-Finnish (FIN) AF: 0.639 AC: 6762 AN: 10586

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.642 AC: 43646 AN: 67974

Other (OTH) AF: 0.605 AC: 1276 AN: 2110

Alfa AF: 0.491 Hom.: 2659

Bravo AF: 0.541

Asia WGS AF: 0.780 AC: 2712 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.9
DANN	Benign	0.45
PhyloP100		-0.072
Mutation Taster		=100/0	polymorphism (auto)

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: rs7288847;

hg19: chr22-46509183;