rs12170325

Variant names:

• chr22-46106990-C-T
• rs12170325
• XM_047441694.1:c.*2401C>T

Variant summary

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

The XM_047441694.1(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_047441694.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.475
• Publications: 12 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=-0.85).
• 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 rank	MANE	Protein	UniProt
LOC124905135	XM_047441694.1	c.*2401C>T		3_prime_UTR_variant	Exon 2 of 2		XP_047297650.1
LOC124905135	XM_047441695.1	c.*2401C>T		3_prime_UTR_variant	Exon 2 of 2		XP_047297651.1
LOC124905135	XM_047441696.1	c.*2401C>T		3_prime_UTR_variant	Exon 2 of 2		XP_047297652.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIRLET7BHG	ENST00000360737.4	n.309-2277C>T		intron_variant	Intron 3 of 4	2
MIRLET7BHG	ENST00000435439.5	n.373-2277C>T		intron_variant	Intron 4 of 5	2
MIRLET7BHG	ENST00000794298.1	n.224-2277C>T		intron_variant	Intron 3 of 5

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

African (AFR) AF: 0.146 AC: 6071 AN: 41540

American (AMR) AF: 0.153 AC: 2346 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 495 AN: 3470

East Asian (EAS) AF: 0.00232 AC: 12 AN: 5170

South Asian (SAS) AF: 0.232 AC: 1120 AN: 4824

European-Finnish (FIN) AF: 0.240 AC: 2544 AN: 10600

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14303 AN: 67990

Other (OTH) AF: 0.172 AC: 364 AN: 2114

Alfa AF: 0.201 Hom.: 6477

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
PhyloP100		-0.47
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs12170325; hg19: chr22-46502870;