rs731085

chr22-46112885-C-Gchr22-46112885-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.*8296C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 487,820 control chromosomes in the GnomAD database, including 41,229 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 0.46 (20036 hom., cov: 33)
  • Exomes 𝑓: 0.34 (21193 hom.)
• Consequence: LOC124905135 XM_047441696.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.359

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124905135	XM_047441696.1	c.*8296C>G		3_prime_UTR_variant	2/2
MIRLET7BHG	NR_027033.2	n.3674C>G		non_coding_transcript_exon_variant	6/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIRLET7BHG	ENST00000360737.4	n.3517C>G		non_coding_transcript_exon_variant	5/5	2

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69887 AN: 152000 Hom.: 19995 Cov.: 33

Gnomad AFR AF: 0.803

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.00366

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.407

GnomAD4 exome AF: 0.336 AC: 112743 AN: 335702 Hom.: 21193 Cov.: 0 AF XY: 0.332 AC XY: 62427 AN XY: 188036

Gnomad4 AFR exome AF: 0.817

Gnomad4 AMR exome AF: 0.256

Gnomad4 ASJ exome AF: 0.323

Gnomad4 EAS exome AF: 0.00180

Gnomad4 SAS exome AF: 0.303

Gnomad4 FIN exome AF: 0.362

Gnomad4 NFE exome AF: 0.355

Gnomad4 OTH exome AF: 0.348

GnomAD4 genome AF: 0.460 AC: 69970 AN: 152118 Hom.: 20036 Cov.: 33 AF XY: 0.453 AC XY: 33703 AN XY: 74356

Gnomad4 AFR AF: 0.803

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.00367

Gnomad4 SAS AF: 0.301

Gnomad4 FIN AF: 0.361

Gnomad4 NFE AF: 0.353

Gnomad4 OTH AF: 0.401

Alfa AF: 0.284 Hom.: 775

Bravo AF: 0.471

Asia WGS AF: 0.208 AC: 724 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.43
Dann	Benign	0.44
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs731085; hg19: chr22-46508765; COSMIC: COSV62450728;