22-46113303-C-T

Position:

• chr22-46113303-C-T

Variant summary

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

The XM_047441696.1(LOC124905135):​c.*8714C>T variant causes a 3 prime UTR 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: LOC124905135 XM_047441696.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720

Genes affected

LOC124905135 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124905135	XM_047441696.1	c.*8714C>T		3_prime_UTR_variant	2/2
MIRLET7BHG	NR_027033.2	n.4092C>T		non_coding_transcript_exon_variant	6/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIRLET7BHG	ENST00000360737.4	n.3935C>T		non_coding_transcript_exon_variant	5/5	2

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

Gnomad4 AFR exome AF: 0.252

Gnomad4 AMR exome AF: 0.664

Gnomad4 ASJ exome AF: 0.705

Gnomad4 EAS exome AF: 0.973

Gnomad4 SAS exome AF: 0.690

Gnomad4 FIN exome AF: 0.655

Gnomad4 NFE exome AF: 0.640

Gnomad4 OTH exome AF: 0.637

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

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.633

Gnomad4 ASJ AF: 0.686

Gnomad4 EAS AF: 0.973

Gnomad4 SAS AF: 0.698

Gnomad4 FIN AF: 0.639

Gnomad4 NFE AF: 0.642

Gnomad4 OTH AF: 0.605

Alfa AF: 0.502 Hom.: 2633

Bravo AF: 0.541

Asia WGS AF: 0.780 AC: 2712 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.9
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7288847; hg19: chr22-46509183;