rs6504230

chr17-64448998-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The 17-64448998-C-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 ENST00000615220.4 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.421

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MILR1	ENST00000615220.4			upstream_gene_variant		2		P1

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

Gnomad4 AFR exome AF: 0.216

Gnomad4 AMR exome AF: 0.433

Gnomad4 ASJ exome AF: 0.583

Gnomad4 EAS exome AF: 0.635

Gnomad4 SAS exome AF: 0.437

Gnomad4 FIN exome AF: 0.436

Gnomad4 NFE exome AF: 0.465

Gnomad4 OTH exome AF: 0.476

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

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.575

Gnomad4 EAS AF: 0.566

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.430

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.457

Alfa AF: 0.431 Hom.: 2208

Bravo AF: 0.385

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
Cadd	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6504230; hg19: -;