rs9905016

Positions:

• 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]

MILR1 (HGNC:):

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/exons	MANE	Protein	UniProt
MILR1	XM_024450708.2	c.*933T>C		3_prime_UTR_variant	10/10		XP_024306476.2
MILR1	XR_002957990.2	n.2082T>C		non_coding_transcript_exon_variant	11/11
		n.64497225T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 25, 2018

- -

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;