rs11703832

chr22-46108287-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.*3698C>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 0.188 in 152,104 control chromosomes in the GnomAD database, including 2,928 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 0.19 (2928 hom., cov: 33)
• Consequence: LOC124905135 XM_047441696.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.89

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124905135	XM_047441696.1	c.*3698C>T		3_prime_UTR_variant	2/2
MIRLET7BHG	NR_027033.2	n.373-980C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIRLET7BHG	ENST00000360737.4	n.309-980C>T		intron_variant, non_coding_transcript_variant		2
MIRLET7BHG	ENST00000435439.5	n.373-980C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28636 AN: 151986 Hom.: 2928 Cov.: 33

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.188 AC: 28643 AN: 152104 Hom.: 2928 Cov.: 33 AF XY: 0.190 AC XY: 14093 AN XY: 74354

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.240

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.180

Alfa AF: 0.212 Hom.: 465

Bravo AF: 0.181

Asia WGS AF: 0.120 AC: 417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.10
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11703832; hg19: chr22-46504167;