rs9905016

Variant names:

• chr17-64497225-T-C
• rs9905016
• XM_024450708.2:c.*933T>C

Your query was ambiguous. Multiple possible variants found:

• chr17-64497225-T-C
• chr17-64497225-T-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The XM_024450708.2(MILR1):​c.*933T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,216 control chromosomes in the GnomAD database, including 11,407 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.28 (11407 hom., cov: 33)
• Consequence: MILR1 XM_024450708.2 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.25

Genes affected

MILR1 (HGNC:27570): (mast cell immunoglobulin like receptor 1) Predicted to enable transmembrane signaling receptor activity. Predicted to be involved in several processes, including cell-cell adhesion via plasma-membrane adhesion molecules; mast cell degranulation; and negative regulation of mast cell activation. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

POLG2 (HGNC:9180): (DNA polymerase gamma 2, accessory subunit) This gene encodes the processivity subunit of the mitochondrial DNA polymerase gamma. The encoded protein forms a heterotrimer containing one catalytic subunit and two processivity subunits. This protein enhances DNA binding and promotes processive DNA synthesis. Mutations in this gene result in autosomal dominant progressive external ophthalmoplegia with mitochondrial DNA deletions.[provided by RefSeq, Sep 2009]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 17-64497225-T-C is Benign according to our data. Variant chr17-64497225-T-C is described in ClinVar as [Benign]. Clinvar id is 1239326.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
POLG2	NM_007215.4	c.-257A>G		upstream_gene_variant		ENST00000539111.7	NP_009146.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POLG2	ENST00000539111.7	c.-257A>G		upstream_gene_variant		1	NM_007215.4	ENSP00000442563.2
POLG2	ENST00000585141.5	n.-206A>G		upstream_gene_variant		1

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42314 AN: 152098 Hom.: 11371 Cov.: 33

Gnomad AFR AF: 0.703

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.0339

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0969

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.279 AC: 42398 AN: 152216 Hom.: 11407 Cov.: 33 AF XY: 0.276 AC XY: 20528 AN XY: 74420

Gnomad4 AFR AF: 0.704

Gnomad4 AMR AF: 0.245

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.0338

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.0969

Gnomad4 OTH AF: 0.219

Alfa AF: 0.140 Hom.: 662

Bravo AF: 0.305

Asia WGS AF: 0.111 AC: 388 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jun 25, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.86
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9905016; hg19: chr17-62493343;