rs13053856

Variant names:

• chr22-46104002-G-A
• rs13053856
• XM_047441694.1:c.523G>A

Your query was ambiguous. Multiple possible variants found:

• chr22-46104002-G-A
• chr22-46104002-G-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.523G>A​(p.Gly175Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 151,350 control chromosomes in the GnomAD database, including 3,812 homozygotes. In-silico tool predicts a benign outcome for this variant. 4/4 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.20 (3812 hom., cov: 34)
• Consequence: LOC124905135 XM_047441694.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.578
• Publications: 5 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000360737.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIRLET7BHG	NR_027033.2		n.372+753G>A		intron	N/A
	MIRLET7BHG	NR_110479.1		n.315-5265G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIRLET7BHG	ENST00000360737.4	TSL:2	n.309-5265G>A		intron	N/A
	MIRLET7BHG	ENST00000381051.7	TSL:2	n.349+753G>A		intron	N/A
	MIRLET7BHG	ENST00000435439.5	TSL:2	n.372+753G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.204 AC: 30784 AN: 151232 Hom.: 3813 Cov.: 34

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.201

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.203 AC: 30783 AN: 151350 Hom.: 3812 Cov.: 34 AF XY: 0.204 AC XY: 15067 AN XY: 73984

African (AFR) AF: 0.107 AC: 4435 AN: 41316

American (AMR) AF: 0.176 AC: 2680 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 670 AN: 3446

East Asian (EAS) AF: 0.00251 AC: 13 AN: 5184

South Asian (SAS) AF: 0.265 AC: 1273 AN: 4812

European-Finnish (FIN) AF: 0.274 AC: 2887 AN: 10526

Middle Eastern (MID) AF: 0.210 AC: 60 AN: 286

European-Non Finnish (NFE) AF: 0.267 AC: 18043 AN: 67546

Other (OTH) AF: 0.200 AC: 421 AN: 2100

Alfa AF: 0.252 Hom.: 842

Bravo AF: 0.193

Asia WGS AF: 0.135 AC: 467 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.7
DANN	Benign	0.77
PhyloP100		0.58
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: rs13053856; hg19: chr22-46499882;