NM_001085423.2:c.-171C>T

Variant names:

• chr17-64448998-C-T
• rs6504230
• NM_001085423.2:c.-171C>T

Variant summary

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

The NM_001085423.2(MILR1):​c.-171C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 391,308 control chromosomes in the GnomAD database, including 40,350 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 0.39 (12282 hom., cov: 25)
  • Exomes 𝑓: 0.48 (28068 hom.)
• Consequence: MILR1 NM_001085423.2 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.421
• Publications: 3 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=0.521).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001085423.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MILR1	NM_001085423.2	MANE Select	c.-171C>T		upstream_gene	N/A	NP_001078892.1	Q7Z6M3-1
	MILR1	NM_001438823.1		c.-171C>T		upstream_gene	N/A	NP_001425752.1
	MILR1	NM_001369493.1		c.-171C>T		upstream_gene	N/A	NP_001356422.1	Q7Z6M3-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MILR1	ENST00000619286.5	TSL:1 MANE Select	c.-171C>T		upstream_gene	N/A	ENSP00000482801.1	Q7Z6M3-1
	MILR1	ENST00000612535.4	TSL:1	c.-171C>T		upstream_gene	N/A	ENSP00000477504.1	Q7Z6M3-3
	MILR1	ENST00000616498.4	TSL:1	c.-171C>T		upstream_gene	N/A	ENSP00000481318.1	Q7Z6M3-2

Frequencies

GnomAD3 genomes AF: 0.386 AC: 57760 AN: 149694 Hom.: 12278 Cov.: 25

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.453

GnomAD4 exome AF: 0.476 AC: 114838 AN: 241496 Hom.: 28068 Cov.: 0 AF XY: 0.476 AC XY: 58293 AN XY: 122420

African (AFR) AF: 0.216 AC: 1489 AN: 6898

American (AMR) AF: 0.433 AC: 3093 AN: 7150

Ashkenazi Jewish (ASJ) AF: 0.583 AC: 5258 AN: 9024

East Asian (EAS) AF: 0.635 AC: 14187 AN: 22356

South Asian (SAS) AF: 0.437 AC: 929 AN: 2126

European-Finnish (FIN) AF: 0.436 AC: 10199 AN: 23372

Middle Eastern (MID) AF: 0.596 AC: 749 AN: 1256

European-Non Finnish (NFE) AF: 0.465 AC: 71359 AN: 153386

Other (OTH) AF: 0.476 AC: 7575 AN: 15928

GnomAD4 genome AF: 0.386 AC: 57772 AN: 149812 Hom.: 12282 Cov.: 25 AF XY: 0.388 AC XY: 28274 AN XY: 72934

African (AFR) AF: 0.194 AC: 7934 AN: 40824

American (AMR) AF: 0.420 AC: 6219 AN: 14812

Ashkenazi Jewish (ASJ) AF: 0.575 AC: 1989 AN: 3458

East Asian (EAS) AF: 0.566 AC: 2827 AN: 4998

South Asian (SAS) AF: 0.416 AC: 1953 AN: 4696

European-Finnish (FIN) AF: 0.430 AC: 4384 AN: 10200

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 30822 AN: 67562

Other (OTH) AF: 0.457 AC: 946 AN: 2070

Alfa AF: 0.436 Hom.: 2929

Bravo AF: 0.385

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	0.52
PhyloP100		-0.42
PromoterAI		-0.26	Neutral

Splicing

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

Other links and lift over

dbSNP: rs6504230;