rs12170325

Positions:

• chr22-46106990-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.*2401C>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 0.181 in 152,216 control chromosomes in the GnomAD database, including 2,762 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 0.18 (2762 hom., cov: 33)
• Consequence: LOC124905135 XM_047441696.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.475

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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124905135	XM_047441696.1	c.*2401C>T		3_prime_UTR_variant	2/2
MIRLET7BHG	NR_027033.2	n.373-2277C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIRLET7BHG	ENST00000360737.4	n.309-2277C>T		intron_variant, non_coding_transcript_variant		2
MIRLET7BHG	ENST00000435439.5	n.373-2277C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27577 AN: 152098 Hom.: 2762 Cov.: 33

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.00232

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.181 AC: 27585 AN: 152216 Hom.: 2762 Cov.: 33 AF XY: 0.183 AC XY: 13640 AN XY: 74422

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.00232

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.240

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.172

Alfa AF: 0.204 Hom.: 4588

Bravo AF: 0.172

Asia WGS AF: 0.130 AC: 452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.2
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12170325; hg19: chr22-46502870;